The scaling of metabolic traits differs among larvae and juvenile colonies of scleractinian corals

Body size profoundly affects organism fitness and ecosystem dynamics through the scaling of physiological traits. This study tests for variation in metabolic scaling and its potential drivers among corals differing in life history strategies and taxonomic identity. Data were compiled from published sources and augmented with empirical measurements of corals in Moorea, French Polynesia. The data compilation revealed metabolic isometry in broadcasted larvae, but size-independent metabolism in brooded larvae; empirical measures of Pocillopora acuta larvae also supported size-independent metabolism in brooded coral larvae. In contrast, for juvenile colonies (i.e., 1-4 cm diameter), metabolic scaling was isometric for Pocillopora spp., and negatively allometric for Porites spp. The scaling of biomass with surface area was isometric for Pocillopora spp., but positively allometric for Porites spp., suggesting the surface area:biomass ratio mediates metabolic scaling in these corals. The scaling of tissue biomass and metabolism were not affected by light treatment (i.e., either natural photoperiods or constant darkness) in both juvenile taxa. However, biomass was reduced by 9-15% in the juvenile corals from the light treatments and this coincided with higher metabolic scaling exponents, thus supporting the causal role of biomass in driving variation in scaling. This study shows that metabolic scaling is plastic in early life stages of corals, with intrinsic differences between life history strategy (i.e., brooded and broadcasted larvae) and taxa (i.e., Pocillopora spp. and Porites spp.), and acquired differences attributed to changes in area-normalized biomass.

Early post-settlement events, rather than settlement, drive recruitment and coral recovery at Moorea, French Polynesia

Understanding population dynamics is a long-standing objective of ecology, but the need for progress in this area has become urgent. For coral reefs, achieving this objective is impeded by a lack of information on settlement versus post-settlement events in determining recruitment and population size. Declines in coral abundance are often inferred to be associated with reduced densities of recruits, which could arise from mechanisms occurring at larval settlement, or throughout post-settlement stages. This study uses annual measurements from 2008 to 2021 of coral cover, the density of coral settlers (S), the density of small corals (SC), and environmental conditions, to evaluate the roles of settlement versus post-settlement events in determining rates of coral recruitment and changes in coral cover at Moorea, French Polynesia. Coral cover, S, SC, and the SC:S ratio (a proxy for post-settlement success), and environmental conditions, were used in generalized additive models (GAMs) to show that: (a) coral cover was more strongly related to SC and SC:S than S, and (b) SC:S was highest when preceded by cool seawater, low concentrations of Chlorophyll a, and low flow speeds, and S showed evidence of declining with elevated temperature. Together, these results suggest that changes in coral cover in Moorea are more strongly influenced by post-settlement events than settlement. The key to understanding coral community resilience may lie in elucidating the factors attenuating the bottleneck between settlers and small corals.

Coral recruitment: patterns and processes determining the dynamics of coral populations

Coral recruitment describes the addition of new individuals to populations, and it is one of the most fundamental demographic processes contributing to population size. As many coral reefs around the world have experienced large declines in coral cover and abundance, there has been great interest in understanding the factors causing coral recruitment to vary and the conditions under which it can support community resilience. While progress in these areas is being facilitated by technological and scientific advances, one of the best tools to quantify recruitment remains the humble settlement tile, variants of which have been in use for over a century. Here I review the biology and ecology of coral recruits and the recruitment process, largely as resolved through the use of settlement tiles, by: (i) defining how the terms 'recruit' and 'recruitment' have been used, and explaining why loose terminology has impeded scientific advancement; (ii) describing how coral recruitment is measured and why settlement tiles have value for this purpose; (iii) summarizing previous efforts to review quantitative analyses of coral recruitment; (iv) describing advances from hypothesis-driven studies in determining how refuges, seawater flow, and grazers can modulate coral recruitment; (v) reviewing the biology of small corals (i.e. recruits) to understand better how they respond to environmental conditions; and (vi) updating a quantitative compilation of coral recruitment studies extending from 1974 to present, thus revealing long-term global declines in density of recruits, juxtaposed with apparent resilience to coral bleaching. Finally, I review future directions in the study of coral recruitment, and highlight the need to expand studies to deliver taxonomic resolution, and explain why time series of settlement tile deployments are likely to remain pivotal in quantifying coral recruitment.

The rising threat of peyssonnelioid algal crusts on coral reefs

For more than a century, coral reefs have been exposed to increasing anthropogenic disturbances that have profoundly altered their community structure. These perturbations continue to challenge coral reefs in new ways as ecological paradigms are recast in the Anthropocene Epoch1. In recent decades, macroalgal blooms have blighted Caribbean reefs2, but the appearance of aggressive peyssonnelioid algal crusts (PAC) that are rapidly increasing in abundance to become dominant members of the benthos on Caribbean and Indo-Pacific reefs is a novel phenomenon in tropical seas3. By pre-empting vacant space, overgrowing corals, deterring the settlement of coral larvae, and favouring a phase transition from coral to algae4, PAC are likely to accelerate the decline in dominance of corals on global reefs (Figure 1).

Asynchrony in coral community structure contributes to reef-scale community stability

Many aspects of global ecosystem degradation are well known, but the ecological implications of variation in these effects over scales of kilometers and years have not been widely considered. On tropical coral reefs, kilometer-scale variation in environmental conditions promotes a spatial mosaic of coral communities in which spatial insurance effects could enhance community stability. To evaluate whether these effects are important on coral reefs, we explored variation over 2006-2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. Coral community structure varied asynchronously among habitats, and variation among habitats in the daily range in seawater temperature suggested it could be a factor contributing to the variation in coral community structure. Wave forced seawater flow connected the habitats and facilitated larval exchange among them, but this effect differed in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation, and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience.

Branching coral morphology affects physiological performance in the absence of colony integration

For nearly 50 years, analyses of coral physiology have used small coral fragments (nubbins) to make inferences about larger colonies. However, scaling in corals shows that linear extrapolations from nubbins to whole colonies can be misleading, because polyps in nubbins are divorced of their morphologically complex and physiologically integrated corallum. We tested for the effects of integration among branches in determining size-dependent calcification of the coral Pocillopora spp. under elevated P_CO2. Area-normalized net calcification was compared between branches (nubbins), aggregates of nubbins (complex morphologies without integration) and whole colonies (physiologically integrated) at 400 versus approximately 1000 µatm P_CO2. Net calcification was unaffected by P_CO2, but differed among colony types. Single nubbins grew faster than whole colonies, but when aggregated, nubbins changed calcification to match whole colonies even though they lacked integration among branches. Corallum morphology causes the phenotype of branching corals to differ from the summation of their branches.

A decade of invertebrate recruitment at Santa Catalina Island, California

Marine fouling communities have long provided model systems for studying the ecology of community development, and settlement plates are the tool of choice for this purpose. Decades of plate deployments provide a baseline against which present-day trends can be interpreted, with one classic trend being the ultimate dominance of plates by colonial and encrusting taxa. Here we report the results of annual deployments of settlement plates from 2010 to 2021 in the shallow sub-tidal of southern California, where the recruitment of invertebrates and algae was recorded photographically, and resolved to functional group (solitary, encrusting, and arborescent) and the lowest taxon possible. The communities on these plates differed among years, with trends in abundances varying by functional group and taxon; solitary taxa consistently were abundant, but encrusting taxa declined in abundance. Seawater temperature and the subsurface concentration of chlorophyll a differed among years, and there was a weak inverse association between temperature and the abundances of encrusting taxa. Long-term increases in seawater temperature therefore could serve as a mechanism causing fouling communities to change. Because of the prominence of encrusting taxa in fouling communities, the shifts in abundance of this functional group reported here may portend ecologically significant changes in fouling communities exposed to warmer seawater because of an alleviation of competition for a classically limiting resource (i.e., space).

Scale dependence of coral reef oases and their environmental correlates

Identifying relatively intact areas within ecosystems and determining the conditions favoring their existence is necessary for effective management in the context of widespread environmental degradation. In this study, we used 3766 surveys of randomly selected sites in the United States and U.S. Territories to identify the correlates of sites categorized as "oases" (defined as sites with relatively high total coral cover). We used occupancy models to evaluate the influence of 10 environmental predictors on the probability that an area (21.2-km² cell) would harbor coral oases defined at four spatial extents: cross-basin, basin, region, and subregion. Across all four spatial extents, oases were more likely to occur in habitats with high light attenuation. The influence of the other environmental predictors on the probability of oasis occurrence were less consistent and varied with the scale of observation. Oases were most likely in areas of low human population density, but this effect was evident only at the cross-basin and subregional extents. At the regional and subregional extents oases were more likely where sea-surface temperature was more variable, whereas at the larger spatial extents the opposite was true. By identifying the correlates of oasis occurrence, the model can inform the prioritization of reef areas for management. Areas with biophysical conditions that confer corals with physiological resilience, as well as limited human impacts, likely support coral reef oases across spatial extents. Our approach is widely applicable to the development of conservation strategies to protect biodiversity and ecosystems in an era of magnified human disturbance.

Persistence of a sessile benthic organism promoted by a morphological strategy combining sheets and trees

Sessile organisms exploit a life-history strategy in which adults are immobile and their growth position is determined at settlement. The morphological strategy exploited by these organisms has strong selective value, because it can allow beneficial matching of morphology to environmental and biological conditions. In benthic marine environments, a 'sheet-tree' morphology is a classic mechanism exploited by select sessile organisms, and milleporine hydrocorals provide one of the best examples of this strategy. Using 30-year analysis of Millepora sp. on the reefs of St. John, US Virgin Islands, I tested for the benefits of a sheet-tree morphology in mediating the ecological success of an important functional group of benthic space holders. The abundance of Millepora sp. chaotically changed from 1992 to 2021 in concert with hurricanes, bleaching and macroalgal crowding. Millepora sp. responded to these disturbances by exploiting their morphological strategy to increase the use of trees when their sheets were compromised by bleaching and spatial competition with macroalgae, and the use of sheets when their trees were broken by storms. Together, these results reveal the selective value of a plastic sheet-tree morphology, which can be exploited by sessile organisms to respond to decadal-scale variation in environmental conditions.

Scaling the effects of ocean acidification on coral growth and coral-coral competition on coral community recovery

Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora, Acropora, Montipora and Porites, model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010-2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100-1,200 µatm pCO₂) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y^-1) of each coral population between 2010-2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y^-1 under ambient conditions and 4.8% y^-1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y^-1, highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains.

Recruitment hotspots and bottlenecks mediate the distribution of corals on a Caribbean reef

Recruitment hotspots are locations where organisms are added to populations at high rates. On tropical reefs where coral abundance has declined, recruitment hotspots are important because they have the potential to promote population recovery. Around St. John, US Virgin Islands, coral recruitment at five sites revealed a hotspot that has persistent for 14 years. Recruitment created a hotspot in density of juvenile corals that was 600 m southeast of the recruitment hotspot. Neither hotspot led to increased coral cover, thus revealing the stringency of the demographic bottleneck impeding progression of recruits to adult sizes and preventing population growth. Recruitment hotspots in low-density coral populations are valuable targets for conservation and sources of corals for restoration.

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in the bleaching response between sympatric cryptic species of the common Indo-Pacific coral, Pocillopora. In April 2019, prolonged ocean heating occurred at Moorea, French Polynesia. 72% of pocilloporid colonies bleached after 22 d of severe heating (>8o C-days) at 10 m depth on the north shore fore reef. Colony mortality ranged from 11% to 42% around the island four months after heating subsided. The majority (86%) of pocilloporids that died from bleaching belonged to a single haplotype, despite twelve haplotypes, representing at least five species, being sampled. Mitochondrial (open reading frame) sequence variation was greater between the haplotypes that experienced mortality versus haplotypes that all survived than it was between nominal species that all survived. Colonies > 30 cm in diameter were identified as the haplotype experiencing the most mortality, and in 1125 colonies that were not genetically identified, bleaching and mortality increased with colony size. Mortality did not increase with colony size within the haplotype suffering the highest mortality, suggesting that size-dependent bleaching and mortality at the genus level was caused instead by differences among cryptic species. The relative abundance of haplotypes shifted between February and August, driven by declines in the same common haplotype for which mortality was estimated directly, at sites where heat accumulation was greatest, and where larger colony sizes occurred. The identification of morphologically indistinguishable species that differ in their response to thermal stress, but share a similar ecological function in terms of maintaining a coral-dominated state, has important consequences for uncovering response diversity that drives resilience, especially in systems with low or declining functional diversity.

Stony coral populations are more sensitive to changes in vital rates in disturbed environments

Reef-building corals, like many long-lived organisms, experience environmental change as a combination of separate but concurrent processes, some of which are gradual yet long-lasting, while others are more acute but short-lived. For corals, some chronic environmental stressors, such as rising temperature and ocean acidification, are thought to induce gradual changes in colonies' vital rates. Meanwhile, other environmental changes, such as the intensification of tropical cyclones, change the disturbance regime that corals experience. Here, we use a physiologically structured population model to explore how chronic environmental stressors that impact the vital rates of individual coral colonies interact with the intensity and magnitude of disturbance to affect coral population dynamics and cover. We find that, when disturbances are relatively benign, intraspecific density dependence driven by space competition partially buffers coral populations against gradual changes in vital rates. However, the impact of chronic stressors is amplified in more highly disturbed environments, because disturbance weakens the buffering effect of space competition. We also show that coral cover is more sensitive to changes in colony growth and mortality than to external recruitment, at least in open populations, and that space competition and size structure mediate the extent and pace of coral population recovery following a large-scale mortality event. Understanding the complex interplay among chronic environmental stressors, mass-mortality events, and population size structure sharpens our ability to manage and to restore coral-reef ecosystems in an increasingly disturbed future.

High ecological resilience of the sea fan Gorgonia ventalina during two severe hurricanes

Since about the turn of the millennium, octocorals have been increasing in abundance on Caribbean reefs. The mechanisms underlying this trend have not been resolved, but the emergent species assemblage appears to be more resilient than the scleractinians they are replacing. The sea fan Gorgonia ventalina is an iconic species in the contemporary octocoral fauna, and here its population dynamics are described from St. John, US Virgin Islands, from 2013 to 2019. Mean densities of G. ventalina at Yawzi Point (9-m depth) varied from 1.4-1.5 colonies m-2, and their mean heights from 24-30 cm; nearby at Tektite (14-m depth), they varied from 0.6-0.8 colonies m-2 and from 25-33 cm. These reefs were impacted by two Category 5 hurricanes in 2017, but neither the density of G. ventalina, the density of their recruits (< 5-cm tall), nor the height of colonies, differed among years, although growth was depressed after the hurricanes. Nevertheless, at Tektite, colony height trended upwards over time, in part because colonies 10.1-20 cm tall were reduced in abundance after the hurricanes. These trends were sustained without density-associated effects mediating recruitment or self-thinning of adults. The dynamics of G. ventalina over seven years reveals the high resilience of this species that will contribute to the persistence of octocorals as a dominant state on Caribbean reefs.

The rise of octocoral forests on Caribbean reefs

Coral reefs throughout the tropics have experienced large declines in the abundance of scleractinian corals over the last few decades, and some reefs are becoming functionally dominated by animal taxa other than scleractinians. This phenomenon is striking on many shallow reefs in the tropical western Atlantic, where arborescent octocorals now are numerically and functionally dominant. Octocorals are one of several taxa that have been overlooked for decades in analyses of coral reef community dynamics, and our understanding of why octocorals are favoured (whereas scleractinians are not) on some modern reefs, and how they will affect the function of future reef communities, is not commensurate with the task of scientifically responding to the coral reef crisis. We summarize the biological and ecological features predisposing octocorals for success under contemporary conditions, and focus on those features that could have generated resistance and resilience of octocoral populations to environmental change on modern reefs. There is a rich set of opportunities for rapid advancement in understanding the factors driving the success of octocorals on modern reefs, but we underscore three lines of inquiry: (1) the functional implications of strongly mixotrophic, polytrophic, and plastic nutrition, (2) the capacity to recruit at high densities and maintain rapid initial rates of vertical growth, and (3) the emergent properties associated with dense animal forests at high colony densities.

Projected shifts in coral size structure in the Anthropocene

Changes in the size structure of coral populations have major consequences for population dynamics and community function, yet many coral reef monitoring projects do not record this critical feature. Consequently, our understanding of current and future trajectories in coral size structure, and the demographic processes underlying these changes, is still emerging. Here, we provide a conceptual summary of the benefits to be gained from more comprehensive attention to the size of coral colonies in reef monitoring projects, and we support our argument through the use of case-history examples and a simplified ecological model. We neither seek to review the available empirical data, or to rigorously explore causes and implications of changes in coral size, we seek to reveal the advantages to modifying ongoing programs to embrace the information inherent in changing coral colony size. Within this framework, we evaluate and forecast the mechanics and implications of changes in the population structure of corals that are transitioning from high to low abundance, and from large to small colonies, sometimes without striking effects on planar coral cover. Using two coral reef locations that have been sampled for coral size, we use demographic data to underscore the limitations of coral cover in understanding the causes and consequences of long-term declining coral size, and abundance. A stage-structured matrix model is used to evaluate the demographic causes of declining coral colony size and abundance, particularly with respect to the risks of extinction. The model revealed differential effects of mortality, growth and fecundity on coral size distributions. It also suggested that colony rarity and declining colony size in association with partial tissue mortality and chronic declines in fecundity, can lead to a demographic bottleneck with the potential to prolong the existence of coral populations when they are characterized by mostly very small colonies. Such bottlenecks could have ecological importance if they can delay extinction and provide time for human intervention to alleviate the environmental degradation driving reductions in coral abundance.

Science-based approach to using growth rate to assess coral performance and restoration outcomes

One response to the coral reef crisis has been human intervention to enhance selection on the fittest corals through cultivation. This requires genotypes to be identified for intervention, with a primary basis for this choice being growth: corals that quickly grow on contemporary reefs might be future winners. To test for temporal stability of growth as a predictor of future performance, genotypes of the coral Porites spp. were grown in common gardens in Mo'orea, French Polynesia. Growth was measured every two to four months throughout 2018, and each period was used as a predictor of growth over the subsequent period. Area-normalized growth explained less than 29% of the variance in subsequent growth, but for biomass-normalized growth this increased to 45-60%, and was highest when summer growth was used to predict autumn growth. The capacity of initial growth to predict future performance is dependent on the units of measurement and the time of year in which it is measured. The final choice of traits to quantify performance must be informed through consideration of the species and the normalization that best capture the information inherent in the biological processes mediating variation in traits values.

Emergent properties of branching morphologies modulate the sensitivity of coral calcification to high PCO2

Experiments with coral fragments (i.e. nubbins) have shown that net calcification is depressed by elevated PCO2 Evaluating the implications of this finding requires scaling of results from nubbins to colonies, yet the experiments to codify this process have not been carried out. Building from our previous research demonstrating that net calcification of Pocillopora verrucosa (2-13 cm diameter) was unaffected by PCO2  (400 and 1000 µatm) and temperature (26.5 and 29.7°C), we sought generality to this outcome by testing how colony size modulates PCO2  and temperature sensitivity in a branching acroporid. Together, these taxa represent two of the dominant lineages of branching corals on Indo-Pacific coral reefs. Two trials conducted over 2 years tested the hypothesis that the seasonal range in seawater temperature (26.5 and 29.2°C) and a future PCO2  (1062 µatm versus an ambient level of 461 µatm) affect net calcification of an ecologically relevant size range (5-20 cm diameter) of colonies of Acropora hyacinthus As for P. verrucosa, the effects of temperature and PCO2  on net calcification (mg day-1) of A. verrucosa were not statistically detectable. These results support the generality of a null outcome on net calcification of exposing intact colonies of branching corals to environmental conditions contrasting seasonal variation in temperature and predicted future variation in PCO2 While there is a need to expand beyond an experimental culture relying on coral nubbins as tractable replicates, rigorously responding to this need poses substantial ethical and logistical challenges.

Resilience of Octocoral Forests to Catastrophic Storms

After centuries of human-mediated disturbances, Caribbean reef communities are vastly different from those described in the 1950s. Many are functionally dominated by macroalgae, but this community state represents only one of several possibilities into which present-day coral reefs can transition. Octocorals have always been abundant on Caribbean reefs, but increases in their abundance over the last few decades suggest that arborescent octocorals have the potential to expand their populations on reefs that hitherto had been dominated by scleractinians. Here we show that octocoral-dominated communities at three sites on the fringing reefs of St. John, US Virgin Islands, were resilient to the effects of two Category 5 hurricanes in 2017. We describe the dynamics of octocoral communities over five years at three sites on shallow reefs (~9-m depth), and test for the effects of Hurricanes Irma and Maria. The hurricanes depressed the densities of juvenile and adult octocoral colonies as much as 47%. However, there were only weak effects on species richness and the relative abundances of the octocoral species. The hurricanes did not alter patterns of spatial variability in octocoral community structure that existed among sites prior to the storms. The density of octocoral recruits (individuals ≤ 5 cm high) was reduced in the year following the hurricanes, mainly due to a decline in abundance of recruits <0.5 cm, but returned to pre-storm densities in 2019. Persistently high octocoral recruitment provides a mechanism supporting ecological resilience of these communities. Continuing environmental degradation is a threat to all tropical marine communities, but the reefs of St. John illustrate how "octocoral forests" can persist as the structurally dominant community on Caribbean reefs.

Implications of high rates of sexual recruitment in driving rapid reef recovery in Mo'orea, French Polynesia

Coral abundance continues to decline on tropical reefs around the world, and this trend suggests that coral reefs may not persist beyond the current century. In contrast, this study describes the near-complete mortality of corals on the outer reef (10 m and 17 m depth) of the north shore of Mo’orea, French Polynesia, from 2005 to 2010, followed by unprecedented recovery from 2011 to 2017. Intense corallivory and a cyclone drove coral cover from 33–48% to <3% by 2010, but over the following seven years, recovery occurred through rapid population growth (up to 12% cover y⁻¹) to 25–74% cover by 2017. The thirteen-year, U-shape trajectory of coral cover over time created by the loss and replacement of millions of corals through sexual reproduction underscores the potential for beneficial genetic responses to environmental conditions for at least one genus, Pocillopora. The high ecological resilience of this coral community appears to have been enhanced by variation among genera in the susceptibility to declining cover, and the capacity for population growth (i.e., response diversity). These results suggest that the outer coral communities of Mo’orea may be poised for genetic changes that could affect their capacity to persistence.

Coral calcifying fluid pH is modulated by seawater carbonate chemistry not solely seawater pH

Reef coral calcification depends on regulation of pH in the internal calcifying fluid (CF) in which the coral skeleton forms. However, little is known about calcifying fluid pH (pH_CF) regulation, despite its importance in determining the response of corals to ocean acidification. Here, we investigate pH_CF in the coral Stylophora pistillata in seawater maintained at constant pH with manipulated carbonate chemistry to alter dissolved inorganic carbon (DIC) concentration, and therefore total alkalinity (A_T). We also investigate the intracellular pH of calcifying cells, photosynthesis, respiration and calcification rates under the same conditions. Our results show that despite constant pH in the surrounding seawater, pH_CF is sensitive to shifts in carbonate chemistry associated with changes in [DIC] and [A_T], revealing that seawater pH is not the sole driver of pH_CF Notably, when we synthesize our results with published data, we identify linear relationships of pH_CF with the seawater [DIC]/[H⁺] ratio, [A_T]/ [H⁺] ratio and [[Formula: see text]]. Our findings contribute new insights into the mechanisms determining the sensitivity of coral calcification to changes in seawater carbonate chemistry, which are needed for predicting effects of environmental change on coral reefs and for robust interpretations of isotopic palaeoenvironmental records in coral skeletons.

Unusually high coral recruitment during the 2016 El Niño in Mo'orea, French Polynesia

The negative implications of the thermal sensitivity of reef corals became clear with coral bleaching throughout the Caribbean in the 1980’s, and later globally, with the severe El Niño of 1998 and extensive seawater warming in 2005. These events have substantially contributed to declines in coral cover, and therefore the El Niño of 2016 raised concerns over the implications for coral reefs; on the Great Barrier Reef these concerns have been realized. A different outcome developed in Mo’orea, French Polynesia, where in situ seawater temperature from 15 March 2016 to 15 April 2016 was an average of 0.4°C above the upper 95% CI of the decadal mean temperature, and the NOAA Degree Heating Weeks (DHW) metric supported a Level 1 bleaching alert (DHW ≥ 4.0). Starting 1 September 2016 and for the rest of the year (122 d), in situ seawater temperature was an average of 0.4°C above the 95% CI of long-term values, although DHW remained at zero. Minor coral bleaching (0.2–2.6% of the coral) occurred on the outer reef (10-m and 17-m depth) in April 2016, by May 2016 it had intensified to affect 1.3–16.8% of the coral, but by August 2016, only 1.4–3.0% of the coral was bleached. Relative to the previous decade, recruitment of scleractinians to settlement tiles on the outer- (10 m) and back- (2 m) reef over 2016/17 was high, both from January 2016 to August 2016, and from August 2016 to January 2017, with increased relative abundances of pocilloporids on the outer reef, and acroporids in the back reef. The 2016 El Niño created a distinctive signature in seawater temperature for Mo’orea, but it did not cause widespread coral bleaching or mortality, rather, it was associated with high coral recruitment. While the 2016 El Niño has negatively affected other coral reefs in the Indo-Pacific, the coral communities of Mo’orea continue to show signs of resilience, thus cautioning against general statements regarding the effects of the 2015/16 El Niño on coral reefs in the region.

Intraspecific variation in growth rate is a poor predictor of fitness for reef corals

Genetic variation underlying differences in organism performance is subject to natural selection, and organisms with high values of genetically determined phenotypic measures of fitness should perform better than those that do not. Using small scleractinian corals (i.e., ≤40-mm diameter), this principle was tested with 20 yr of census data from St. John, US Virgin Islands. Using growth rate (change in diameter) as a measure of fitness, growth in one year was tested for association with growth and survivorship in the following two years, and this process was repeated over 20 yr using a 3-yr sliding window. Virtually all variation in growth was independent of colony size, and growth among pairs of years was highly variable, with corals that grew fast in one year rarely growing fast in the next 2 yr. While growth in some pairs of years was positively correlated, ≤4% of the growth variance was explained by growth in the preceding 2 yr. Survivorship was related positively to growth in the preceding year, but the association was weak, it did not extend over 3 yr, and was inconsistent over the study. These results demonstrate the importance of the environment in translating phenotypic measures of fitness into future performance, and for small Caribbean corals, they suggest that environmental conditions may preempt genotype in determining short-term success.

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.

Effects of Temperature and pCO2 on Population Regulation of Symbiodinium spp. in a Tropical Reef Coral

This study tested the bleaching response of the Pacific coral Seriatopora caliendrum to short-term exposure to high temperature and elevated partial pressure of carbon dioxide (pCO₂). Juvenile colonies collected from Nanwan Bay, Taiwan, were used in a factorial experimental design in which 2 temperatures (∼27.6 °C and ∼30.4 °C) and 2 pCO₂ values (∼47.2 Pa and ∼90.7 Pa) were crossed to evaluate, over 12 days, the effects on the densities and physiology of the symbiotic dinoflagellates (Symbiodinium) in the corals. Thermal bleaching, as defined by a reduction of Symbiodinium densities at high temperature, was unaffected by high pCO₂. The division, or mitotic index (MI), of Symbiodinium remaining in thermally bleached corals was about 35% lower than in control colonies, but they contained about 53% more chlorophyll. Bleaching was highly variable among colonies, but the differences were unrelated to MI or pigment content of Symbiodinium remaining in the coral host. At the end of the study, all of the corals contained clade C Symbiodinium (either C1d or C15), and the genetic variation of symbionts did not account for among-colony bleaching differences. These results showed that high temperature causes coral bleaching independent of pCO₂, and underscores the potential role of the coral host in driving intraspecific variation in coral bleaching.

Conspecific aggregations mitigate the effects of ocean acidification on calcification of the coral Pocillopora verrucosa

In densely populated communities, such as coral reefs, organisms can modify the physical and chemical environment for neighbouring individuals. We tested the hypothesis that colony density (12 colonies each placed ∼0.5 cm apart versus ∼8 cm apart) can modulate the physiological response (measured through rates of calcification, photosynthesis and respiration in the light and dark) of the coral Pocillopora verrucosa to partial pressure of CO₂ (P_CO2 ) treatments (∼400 μatm and ∼1200 μatm) by altering the seawater flow regimes experienced by colonies placed in aggregations within a flume at a single flow speed. While light calcification decreased 20% under elevated versus ambient P_CO2  for colonies in low-density aggregations, light calcification of high-density aggregations increased 23% at elevated versus ambient P_CO2 As a result, densely aggregated corals maintained calcification rates over 24 h that were comparable to those maintained under ambient P_CO2 , despite a 45% decrease in dark calcification at elevated versus ambient P_CO2 Additionally, densely aggregated corals experienced reduced flow speeds and higher seawater retention times between colonies owing to the formation of eddies. These results support recent indications that neighbouring organisms, such as the conspecific coral colonies in the present example, can create small-scale refugia from the negative effects of ocean acidification.

The potential for self-seeding by the coral Pocillopora spp. in Moorea, French Polynesia

Coral reefs in Moorea, French Polynesia, suffered catastrophic coral mortality through predation by Acanthaster planci from 2006 to 2010, and Cyclone Oli in 2010, yet by 2015 some coral populations were approaching pre-disturbance sizes. Using long-term study plots, we quantified population dynamics of spawning Pocillopora spp. along the north shore of Moorea between 2010 and 2014, and considered evidence that population recovery could be supported by self-seeding. Results scaled up from study plots and settlement tiles suggest that the number of Pocillopora spp. colonies on the outer reef increased 1,890-fold between 2010 and 2014/2015, and in the back reef, 8-fold between 2010 and 2014/2015. Assuming that spawning Pocillopora spp. in Moorea release similar numbers of eggs as con-generics in Hawaii, and fertilization success is similar to other spawning corals, the capacity of Pocillopora spp. to produce larvae was estimated. These estimates suggest that Pocillopora spp. in Moorea produced a large excess of larvae in 2010 and 2014 relative to the number required to produce the recruits found in the back reef and outer reef in 2010 and 2014, even assuming that ∼99.9% of the larvae do not recruit in Moorea. Less than a third of the recruits in one year would have to survive to produce the juvenile Pocillopora spp. found in the back and outer reefs in 2010 and 2014/2015. Our first order approximations reveal the potential for Pocillopora spp. on the north shore of Moorea to produce enough larvae to support local recruitment and population recovery following a catastrophic disturbance.

Size-dependent physiological responses of the branching coral Pocillopora verrucosa to elevated temperature and PCO2

Body size has large effects on organism physiology, but these effects remain poorly understood in modular animals with complex morphologies. Using two trials of a ∼24 day experiment conducted in 2014 and 2015, we tested the hypothesis that colony size of the coral Pocillopora verrucosa affects the response of calcification, aerobic respiration and gross photosynthesis to temperature (∼26.5 and ∼29.7°C) and P_CO2  (∼40 and ∼1000 µatm). Large corals calcified more than small corals, but at a slower size-specific rate; area-normalized calcification declined with size. Whole-colony and area-normalized calcification were unaffected by temperature, P_CO2 , or the interaction between the two. Whole-colony respiration increased with colony size, but the slopes of these relationships differed between treatments. Area-normalized gross photosynthesis declined with colony size, but whole-colony photosynthesis was unaffected by P_CO2 , and showed a weak response to temperature. When scaled up to predict the response of large corals, area-normalized metrics of physiological performance measured using small corals provide inaccurate estimates of the physiological performance of large colonies. Together, these results demonstrate the importance of colony size in modulating the response of branching corals to elevated temperature and high P_CO2.

Framework of barrier reefs threatened by ocean acidification

To date, studies of ocean acidification (OA) on coral reefs have focused on organisms rather than communities, and the few community effects that have been addressed have focused on shallow back reef habitats. The effects of OA on outer barrier reefs, which are the most striking of coral reef habitats and are functionally and physically different from back reefs, are unknown. Using 5-m long outdoor flumes to create treatment conditions, we constructed coral reef communities comprised of calcified algae, corals, and reef pavement that were assembled to match the community structure at 17 m depth on the outer barrier reef of Moorea, French Polynesia. Communities were maintained under ambient and 1200 μatm pCO2 for 7 weeks, and net calcification rates were measured at different flow speeds. Community net calcification was significantly affected by OA, especially at night when net calcification was depressed ~78% compared to ambient pCO2 . Flow speed (2-14 cm s(-1) ) enhanced net calcification only at night under elevated pCO2 . Reef pavement also was affected by OA, with dissolution ~86% higher under elevated pCO2 compared to ambient pCO2 . These results suggest that net accretion of outer barrier reef communities will decline under OA conditions predicted within the next 100 years, largely because of increased dissolution of reef pavement. Such extensive dissolution poses a threat to the carbonate foundation of barrier reef communities.

The implications of reduced metabolic rate in a resource-limited coral

Many organisms exhibit depressed metabolism when resources are limited, a change that makes it possible to balance an energy budget. For symbiotic reef corals, daily cycles of light and periods of intense cloud cover can be chronic causes of food limitation through reduced photosynthesis. Furthermore, coral bleaching is common in present day reefs, creating a context in which metabolic depression could have beneficial value to corals. In the present study, corals (massive Porites) were exposed to an extreme case of resource limitation by starving them of food and light for 20 d. When resources were limited, the corals depressed area-normalized respiration to 37% of initial rates, coral biomass declined to 64% of initial amounts, yet the corals continued to produce skeletal mass. However, the declines in biomass cannot account for the declines in area-normalized respiration, as mass-specific respiration declined to 30% of initial rates. Thus, these corals appear to be capable of metabolic depression. It is possible that some coral species are better able to depress metabolic rates, such variation could explain differential survival during conditions that limit resources (e.g., shading). Furthermore, we found that maintenance of existing biomass, in part, supports the production of skeletal mass. This association could be explained if maintenance supplies needed energy (e.g., ATP) or inorganic carbon (i.e., CO2) that otherwise limits the production of skeletal mass. Finally, the observed metabolic depression can be explained as change in pool sizes, and does not require a change in metabolic rules.

Pacific-wide contrast highlights resistance of reef calcifiers to ocean acidification

Ocean acidification (OA) and its associated decline in calcium carbonate saturation states is one of the major threats that tropical coral reefs face this century. Previous studies of the effect of OA on coral reef calcifiers have described a wide variety of outcomes for studies using comparable partial pressure of CO2 (pCO2) ranges, suggesting that key questions remain unresolved. One unresolved hypothesis posits that heterogeneity in the response of reef calcifiers to high pCO2 is a result of regional-scale variation in the responses to OA. To test this hypothesis, we incubated two coral taxa (Pocillopora damicornis and massive Porites) and two calcified algae (Porolithon onkodes and Halimeda macroloba) under 400, 700 and 1000 μatm pCO2 levels in experiments in Moorea (French Polynesia), Hawaii (USA) and Okinawa (Japan), where environmental conditions differ. Both corals and H. macroloba were insensitive to OA at all three locations, while the effects of OA on P. onkodes were location-specific. In Moorea and Hawaii, calcification of P. onkodes was depressed by high pCO2, but for specimens in Okinawa, there was no effect of OA. Using a study of large geographical scale, we show that resistance to OA of some reef species is a constitutive character expressed across the Pacific.

Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

Persistence and change in community composition of reef corals through present, past, and future climates

The reduction in coral cover on many contemporary tropical reefs suggests a different set of coral community assemblages will dominate future reefs. To evaluate the capacity of reef corals to persist over various time scales, we examined coral community dynamics in contemporary, fossil, and simulated future coral reef ecosystems. Based on studies between 1987 and 2012 at two locations in the Caribbean, and between 1981 and 2013 at five locations in the Indo-Pacific, we show that many coral genera declined in abundance, some showed no change in abundance, and a few coral genera increased in abundance. Whether the abundance of a genus declined, increased, or was conserved, was independent of coral family. An analysis of fossil-reef communities in the Caribbean revealed changes in numerical dominance and relative abundances of coral genera, and demonstrated that neither dominance nor taxon was associated with persistence. As coral family was a poor predictor of performance on contemporary reefs, a trait-based, dynamic, multi-patch model was developed to explore the phenotypic basis of ecological performance in a warmer future. Sensitivity analyses revealed that upon exposure to thermal stress, thermal tolerance, growth rate, and longevity were the most important predictors of coral persistence. Together, our results underscore the high variation in the rates and direction of change in coral abundances on contemporary and fossil reefs. Given this variation, it remains possible that coral reefs will be populated by a subset of the present coral fauna in a future that is warmer than the recent past.

Evidence that high pCO2 affects protein metabolism in tropical reef corals

Early life stages of the coral Seriatopora caliendrum were used to test the hypothesis that the depression of dark respiration in coral recruits by high pCO2 is caused by perturbed protein metabolism. First, the contribution of protein anabolism to respiratory costs under high pCO2 was evaluated by measuring the aerobic respiration of S. caliendrum recruits with and without the protein synthesis inhibitor emetine following 1 to 4 days at 45 Pa versus 77 Pa pCO2. Second, protein catabolism under high pCO2 was evaluated by measuring the flux of ammonium (NH4 (+)) from juvenile colonies of S. caliendrum incubated in darkness at 47 Pa and 90 Pa pCO2. Two days after settlement, respiration of recruits was affected by an interaction between emetine and pCO2, with emetine reducing respiration 63% at 45 Pa pCO2 and 27% at 77 Pa pCO2. The interaction disappeared 5 days after settlement, when respiration was reduced 27% by emetine under both pCO2 conditions. These findings suggest that protein anabolism accounted for a large proportion of metabolic costs in coral recruits and was affected by high pCO2, with consequences detected in aerobic respiration. Juvenile S. caliendrum showed net uptake of NH4 (+) at 45 Pa pCO2 but net release of NH4 (+) at 90 Pa pCO2, indicating that protein catabolism, NH4 (+) recycling, or both were affected by high pCO2. Together, these results are consistent with the hypothesis that high pCO2 affects protein metabolism in corals.

In situ effects of low pH and elevated HCO3- on juvenile massive Porites spp. in Moorea, French Polynesia

Juvenile colonies of massive Porites spp. were exposed to manipulated pH and bicarbonate ([HCO3-]) in situ to test the hypothesis that ocean acidification (OA) does not affect respiration and calcification. Incubations lasted 28 h and exposed corals to ambient temperature and light with ecologically relevant water motion. Three treatments were applied: (1) ambient conditions of pH 8.04 and 1751 μmol HCO3- kg(-1) (Treatment 1), (2) pCO2-induced ocean acidification of pH 7.73 and 2011 μmol HCO3- kg(-1) (Treatment 2), and (3) pCO2 and HCO3--enriched seawater of pH 7.69 and 2730 μmol HCO3- kg(-1) (Treatment 3). The third treatment providing elevated [HCO3-] was used to test for stimulatory effects of dissolved inorganic carbon on calcification under low pH and low saturation of aragonite (Ωarag), but it does not reflect conditions expected to occur under CO2-driven OA. Calcification of juvenile massive Porites spp. was affected by treatments, with an 81% elevation in Treatment 3 versus Treatment 1, but no difference between Treatments 1 and 2; respiration and the metabolic expenditure concurrent with calcification remained unaffected. These findings indicate that juvenile massive Porites spp. are resistant to short exposures to OA in situ, and separately, that they can increase calcification at low pH and low Ωarag if [HCO3-] is elevated. Juvenile Porites spp. may therefore be limited by dissolved inorganic carbon under ambient pCO2 conditions.

The role of light in mediating the effects of ocean acidification on coral calcification

We tested the effect of light and pCO2 on the calcification and survival of Pocillopora damicornis recruits settled from larvae released in southern Taiwan. In March 2011, recruits were incubated at 31, 41, 70, 122, and 226 μmol photons m-2s-1 under ambient (493 μatm) and high pCO2 (878 μatm). After 5 days calcification was measured gravimetrically and survivorship estimated as the number of living recruits. Calcification was affected by the interaction of pCO2 with light, and at 493 μatm pCO2 the response to light intensity resembled a positive parabola. At 878 μatm pCO2, the effect of light on calcification differed from that observed at 493 μatm pCO2, with the result that there were large differences in calcification between 493 μatm and 878 μatm pCO2 at intermediate light intensities (ca. 70 μmol photons m-2s-1), but similar rates of calcification at the highest and lowest light intensities. Survivorship was affected by light and pCO2, and was highest at 122 μmol photons m-2s-1 in both pCO2 treatments, but was unrelated to calcification. In June 2012 the experiment was repeated, and again the results suggested that exposure to high pCO2 decreased calcification of P. damicornis recruits at intermediate light intensities, but not at lower or higher intensities. Together, our findings demonstrate that the effect of pCO2 on coral recruits can be light-dependent, with inhibitory effects of high pCO2 on calcification at intermediate light intensities that disappear at both higher and lower light intensities.

Coral reef calcifiers buffer their response to ocean acidification using both bicarbonate and carbonate

Central to evaluating the effects of ocean acidification (OA) on coral reefs is understanding how calcification is affected by the dissolution of CO(2) in sea water, which causes declines in carbonate ion concentration [CO(3)(2-)] and increases in bicarbonate ion concentration [HCO(3)(-)]. To address this topic, we manipulated [CO(3)(2-)] and [HCO(3)(-)] to test the effects on calcification of the coral Porites rus and the alga Hydrolithon onkodes, measured from the start to the end of a 15-day incubation, as well as in the day and night. [CO(3)(2-)] played a significant role in light and dark calcification of P. rus, whereas [HCO(3)(-)] mainly affected calcification in the light. Both [CO(3)(2-)] and [HCO(3)(-)] had a significant effect on the calcification of H. onkodes, but the strongest relationship was found with [CO(3)(2-)]. Our results show that the negative effect of declining [CO(3)(2-)] on the calcification of corals and algae can be partly mitigated by the use of HCO(3)(-) for calcification and perhaps photosynthesis. These results add empirical support to two conceptual models that can form a template for further research to account for the calcification response of corals and crustose coralline algae to OA.

Photophysiological consequences of vertical stratification of Symbiodinium in tissue of the coral Porites lutea

In comparison to some corals, massive Porites spp. is physiologically resilient to environmental assaults and is becoming more abundant on coral reefs. To evaluate the extent to which thick tissues contribute to this physiological resilience, we tested the hypothesis that the Symbiodinium in Porites lutea are phenotypically and genetically homogeneous with regard to their distribution vertically within the tissue, and in their response to temperature. Symbiodinium density, genetic identity, and photophysiology were compared between outer and inner tissues defined as adjacent layers ~2 mm thick and beneath the skeleton surface. Symbiodinium densities were 5-fold greater and their cells contained less chlorophyll a in outer versus inner tissue, but ITS2 sequence identities were genetically uniform between layers. Maximum photochemical efficiency (F(v)/F(m)) in inner and outer tissue from the top and sides of the corals differed 6%-7%, with F(v)/F(m) greater in inner versus outer tissue on the top of colonies. On the tops of colonies, the initial slopes of the rETR versus irradiance relationship were not different between tissue layers, although they tended to be less steep for inner tissue. When exposed for 12 h to 28 °C, 30 °C, or 32 °C at ~700 μmol quanta m(-2) s(-1), there was a trend for F(v)/F(m) of the Symbiodinium in both tissue layers to be reduced at 32 °C. Our results do not conform well to shade acclimatization in inner versus outer tissue of P. lutea, and they imply within-tissue heterogeneity that may be an important determinant of physiological performance in perforate corals.