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Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturbations, such as pollution and overfishing, and widespread phenomena, such as bleaching. Here, we report on the history of the Jakarta Bay-Thousand Islands reef system from 1985 to 2011. Over this period, we recorded significant shifts in coral generic composition and an overall decline in coral cover with widely different trajectories between in-, mid- and offshore zones. In 1985, coral cover exhibited a clear on-to-offshore gradient with low coral cover inshore (10%), moderate cover midshore (49%) and high cover offshore (74%). The low coral cover inshore contrasts strongly with reports of high coral cover for inshore reefs in 1929. Inshore, coral cover declined from 10% in 1985 to <5% in 1995. The greatest change in coral cover and composition, however, occurred in offshore reefs, where mean cover declined from 74 to <20% between 1985 and 1995. Acropora species were particularly affected and declined from 36 to just 5% cover offshore. Recovery of coral cover occurred offshore between 1995 and 2005. From 2005 to 2011, however, a less severe loss in coral cover was observed. With the exception of inshore reefs, which appear to be on an ongoing trajectory of decline that started before the 1985 surveys, the reefs of the Jakarta Bay-Thousand Islands system have shown a propensity to recover.

For many corals, the timing of broadcast spawning correlates strongly with a number of environmental signals (seasonal temperature, lunar, and diel cycles). Robust experimental studies examining the role of these putative cues in triggering spawning have been lacking until recently because it has not been possible to predictably induce spawning in fully closed artificial mesocosms. Here, we present a closed system mesocosm aquarium design that utilizes microprocessor technology to accurately replicate environmental conditions, including photoperiod, seasonal insolation, lunar cycles, and seasonal temperature from Singapore and the Great Barrier Reef (GBR), Australia. Coupled with appropriate coral husbandry, these mesocosms were successful in inducing, for the first time, broadcast coral spawning in a fully closed artificial ex situ environment. Four Acropora species (A. hyacinthus, A. tenuis, A. millepora, and A. microclados) from two geographical locations, kept for over 1 year, completed full gametogenic cycles ex situ. The percentage of colonies developing oocytes varied from ~29% for A. hyacinthus to 100% for A. millepora and A. microclados. Within the Singapore mesocosm, A. hyacinthus exhibited the closest synchronization to wild spawning, with all four gravid colonies releasing gametes in the same lunar month as wild predicted dates. Spawning within the GBR mesocosm commenced at the predicted wild spawn date but extended over a period of 3 months. Gamete release in relation to the time postsunset for A. hyacinthus, A. millepora, and A. tenuis was consistent with time windows previously described in the wild. Spawn date in relation to full moon, however, was delayed in all species, possibly as a result of external light pollution. The system described here could broaden the number of institutions on a global scale, that can access material for broadcast coral spawning research, providing opportunities for institutions distant from coral reefs to produce large numbers of coral larvae and juveniles for research purposes and reef restoration efforts. Here, we present a novel design for a mesocosm that can replicate ex situ environmental parameters (seasonal SST, photoperiod, lunar cycle, and insolation) aimed to facilitate controlled spawning events in four species of broadcast spawning corals from two geographically distinct locations: Singapore and the Great Barrier Reef (GBR). This system allowed us, with a strict tailored husbandry protocol, to complete full gametogenic cycle and successfully spawn all four Acroporid species in a fully closed artificial ex situ environment.

Mesophotic coral ecosystems (i.e., deep coral reefs at 30–120 m depth) appear to be thriving while many shallow reefs in the world are declining. Amid efforts to understand and manage their decline, it was suggested that mesophotic reefs might serve as natural refuges and a possible source of propagules for the shallow reefs. However, our knowledge of how reproductive performance of corals alters with depth is sparse. Here, we present a comprehensive study of the reproductive phenology, fecundity, and abundance of seven reef-building conspecific corals in shallow and mesophotic habitats. Significant differences were found in the synchrony and timing of gametogenesis and spawning between shallow and mesophotic coral populations. Thus, mesophotic populations exhibited delayed or protracted spawning events, which led to spawning of the mesophotic colonies in large proportions at times where the shallow ones had long been depleted of reproductive material. All species investigated demonstrated a substantial reduction in fecundity and/or oocyte sizes at mesophotic depths (40–60 m). Two species (Seriatopora hystrix and Galaxea fascicularis) displayed a reduction in both fecundity and oocyte size at mesophotic depths. Turbinaria reniformis had only reduced fecundity and Acropora squarrosa and Acropora valida only reduced oocyte size. In Montipora verrucosa, reduced fecundity was found during one annual reproductive season while, in the following year, only reduced oocyte size was found. In contrast, reduced oocyte size in mesophotic populations of Acropora squarrosa was consistent along three studied years. One species, Acropora pharaonis, was found to be infertile at mesophotic depths along two studied years. This indicates that reproductive performance decreases with depth; and that although some species are capable of reproducing at mesophotic depths, their contribution to the replenishment of shallow reefs may be inconsequential. Reduced reproductive performance with depth, combined with the possible narrower tolerance to environmental factors, further suggests that mesophotic corals may in fact be more vulnerable than previously conceived. Furthermore, we posit that the observed temporal segregation in reproduction could lead to assortative mating, and this, in turn, may facilitate adaptive divergence across depth.

Coral diseases represent a significant and increasing threat to coral reefs. Among the most destructive diseases is White Syndrome (WS), which is increasing in distribution and prevalence throughout the Indo-Pacific. The aim of this study was to determine taxonomic and spatial patterns in mortality rates of corals following the 2008 outbreak of WS at Christmas Island in the eastern Indian Ocean. WS mainly affected Acropora plate corals and caused total mortality of 36% of colonies across all surveyed sites and depths. Total mortality varied between sites but was generally much greater in the shallows (0-96% of colonies at 5 m depth) compared to deeper waters (0-30% of colonies at 20 m depth). Site-specific mortality rates were a reflection of the proportion of corals affected by WS at each site during the initial outbreak and were predicted by the initial cover of live Acropora plate cover. The WS outbreak had a selective impact on the coral community. Following the outbreak, live Acropora plate coral cover at 5 m depth decreased significantly from 7.0 to 0.8%, while the cover of other coral taxa remained unchanged. Observations five years after the initial outbreak revealed that total Acropora plate cover remained low and confirmed that corals that lost all their tissue due to WS did not recover. These results demonstrate that WS represents a significant and selective form of coral mortality and highlights the serious threat WS poses to coral reefs in the Indo-Pacific.

Tropical reefs are dynamic ecosystems that host diverse coral assemblages with different life-history strategies. Here, we quantified how juvenile (<50 mm) coral demographics influenced benthic coral structure in reef flat and reef slope habitats on the southern Great Barrier Reef, Australia. Permanent plots and settlement tiles were monitored every six months for three years in each habitat. These environments exhibited profound differences: the reef slope was characterised by 95% less macroalgal cover, and twice the amount of available settlement substrata and rates of coral settlement than the reef flat. Consequently, post-settlement coral survival in the reef slope was substantially higher than that of the reef flat, and resulted in a rapid increase in coral cover from 7 to 31% in 2.5 years. In contrast, coral cover on the reef flat remained low (~10%), whereas macroalgal cover increased from 23 to 45%. A positive stock-recruitment relationship was found in brooding corals in both habitats; however, brooding corals were not directly responsible for the observed changes in coral cover. Rather, the rapid increase on the reef slope resulted from high abundances of broadcast spawning Acropora recruits. Incorporating our results into transition matrix models demonstrated that most corals escape mortality once they exceed 50 mm, but for smaller corals mortality in brooders was double those of spawners (i.e. acroporids and massive corals). For corals on the reef flat, sensitivity analysis demonstrated that growth and mortality of larger juveniles (21-50 mm) highly influenced population dynamics; whereas the recruitment, growth and mortality of smaller corals (<20 mm) had the highest influence on reef slope population dynamics. Our results provide insight into the population dynamics and recovery trajectories in disparate reef habitats, and highlight the importance of acroporid recruitment in driving rapid increases in coral cover following large-scale perturbation in reef slope environments.

Concern for the future of reef-building corals in conditions of rising sea temperatures combined with recent technological advances has led to a renewed interest in documenting the biodiversity of mesophotic coral ecosystems (MCEs) and their potential to provide lineage continuation for coral taxa. Here, we examine species diversity of staghorn corals (genera Acropora and Isopora) in the mesophotic zone (below 30 m depth) of the Great Barrier Reef and western Coral Sea. Using specimen-based records we found 38 staghorn species in the mesophotic zone, including three species newly recorded for Australia and five species that only occurred below 30 m. Staghorn corals became scarce at depths below 50 m but were found growing in-situ to 73 m depth. Of the 76 staghorn coral species recorded for shallow waters (depth less than or equal to 30 m) in north-east Australia, 21% extended to mesophotic depths with a further 22% recorded only rarely to 40 m depth. Extending into the mesophotic zone provided shallow water species no significant advantage in terms of their estimated global range-size relative to species restricted to shallow waters (means 86.2 X 106 km2 and 85.7 X 106 km2 respectively, p = 0.98). We found four staghorn coral species at mesophotic depths on the Great Barrier Reef that were previously considered rare and endangered on the basis of their limited distribution in central Indonesia and the far western Pacific. Colonies below 40 m depth showed laterally flattened branches, light and fragile skeletal structure and increased spacing between branches and corallites. The morphological changes are discussed in relation to decreased light, water movement and down-welling coarse sediments. Staghorn corals have long been regarded as typical shallow-water genera, but here we demonstrate the significant contribution of this group to the region's mesophotic fauna and the importance of considering MCEs in reef biodiversity estimates and management.

Coral reef ecosystems are based on coral-zooxanthellae symbiosis. During the initiation of symbiosis, majority of corals acquire their own zooxanthellae (specifically from the dinoflagellate genus Symbiodinium) from surrounding environments. The mechanisms underlying the initial establishment of symbiosis have attracted much interest, and numerous field and laboratory experiments have been conducted to elucidate this establishment. However, it is still unclear whether the host corals selectively or randomly acquire their symbionts from surrounding environments. To address this issue, we initially compared genetic compositions of Symbiodinium within naturally settled about 2-week-old Acropora coral juveniles (recruits) and those in the adjacent seawater as the potential symbiont source. We then performed infection tests using several types of Symbiodinium culture strains and apo-symbiotic (does not have Symbiodinium cells yet) Acropora coral larvae. Our field observations indicated apparent preference toward specific Symbiodinium genotypes (A1 and D1-4) within the recruits, despite a rich abundance of other Symbiodinium in the environmental population pool. Laboratory experiments were in accordance with this field observation: Symbiodinium strains of type A1 and D1-4 showed higher infection rates for Acropora larvae than other genotype strains, even when supplied at lower cell densities. Subsequent attraction tests revealed that three Symbiodinium strains were attracted toward Acropora larvae, and within them, only A1 and D1-4 strains were acquired by the larvae. Another three strains did not intrinsically approach to the larvae. These findings suggest the initial establishment of corals-Symbiodinium symbiosis is not random, and the infection mechanism appeared to comprise two steps: initial attraction step and subsequent selective uptake by the coral.

Coral reefs are facing a biodiversity crisis due to increasing human impacts, consequently, one third of reef-building corals have an elevated risk of extinction. Logistic challenges prevent broad-scale species-level monitoring of hard corals; hence it has become critical that effective proxy indicators of species richness are established. This study tests how accurately three potential proxy indicators (generic richness on belt transects, generic richness on point-intercept transects and percent live hard coral cover on point-intercept transects) predict coral species richness at three different locations and two analytical scales. Generic richness (measured on a belt transect) was found to be the most effective predictor variable, with significant positive linear relationships across locations and scales. Percent live hard coral cover consistently performed poorly as an indicator of coral species richness. This study advances the practical framework for optimizing coral reef monitoring programs and empirically demonstrates that generic richness offers an effective way to predict coral species richness with a moderate level of precision. While the accuracy of species richness estimates will decrease in communities dominated by species-rich genera (e.g. Acropora), generic richness provides a useful measure of phylogenetic diversity and incorporating this metric into monitoring programs will increase the likelihood that changes in coral species diversity can be detected.

While there is increasing evidence for habitat specialization in coral reef fishes, the extent to which different corals support different fish communities is not well understood. Here we quantitatively assess the relative importance of different coral species in structuring fish communities and evaluate whether sampling scale and coral colony size affect the perceived strength of fish-habitat relationships. Fish communities present on colonies of eight coral species (Porites cylindrica, Echinopora horrida, Hydnophora rigida, Stylophora pistillata, Seriatopora hystrix, Acropora formosa, A. tenuis and A. millepora) were examined in the Lizard Island lagoon, Great Barrier Reef, Australia. Additionally, the differences in fish communities supported by three coral species (P. cylindrica, E. horrida, H. rigida) were investigated at three spatial scales of sampling (2x2 m, 1x1 m, 0.5x0.5 m). Substantial differences in fish communities were observed across the different coral species, with E. horrida and H. rigida supporting the most fish species and individuals. Coral species explained more of the variability in fish species richness (20.9–53.6%), than in fish abundance (0–15%). Most coral species supported distinctive fish communities, with dissimilarities ranging from 50 to 90%. For three focal coral species, a greater amount of total variation in fish species richness and fish abundance was evident at a larger scale of sampling. Together, these results indicate that the structure of reef fish communities is finely tuned to coral species. Loss of preferred coral species could have profound effects on reef fish biodiversity, potentially more so than would be predicted on the basis of declining coral cover alone.

Heterotrophic feeding in newly-settled coral planulae can potentially improve survivorship and accelerate early development in some species; however, an optimal diet to facilitate this does not currently exist. This study evaluated the efficacy of three heterotrophic feeding regimes (enriched rotifers, unfiltered seawater, and a novel, particulate diet), against a wholly-phototrophic treatment on Acropora hyacinthus, A. loripes, A. millepora, and A. tenuis recruits, over 93 days post-settlement. The unfiltered seawater treatment recorded maximum survival for all species (A. hyacinthus 95.9±8.0%, A. loripes: 74.3±11.5%, A. millepora: 67±12.7%, A. tenuis: 53.2±11.3%), although not significant. Growth (% surface area gain) was also greatest in the unfiltered seawater, and this was significant for A. millepora (870±307%) and A. tenuis (693±91.8%) (p<0.05). Although total lipid concentration was relatively stable across treatments, the lipid class composition exhibited species-specific responses to each treatment. Lower saturated and higher polyunsaturated fatty acids appeared beneficial to recruit performance, particularly in the unfiltered seawater, which generally contained the highest levels of 20:5n-3 (EPA), 22:6n-3 (DHA), and 20:4n-6 (ARA). The present study demonstrates the capacity of a nutritionally adequate and readily accepted heterotrophic feeding regime to increase coral recruit survival, growth, and health, which can greatly reduce the time required in cost- and labour-intensive culture.