Abstract Linear regressions between total alkalinity (TA) and dissolved inorganic carbon (DIC) are widely used to infer the balance between net ecosystem calcification (NEC) and net ecosystem production (NEP) in coral reefs. Using high‐frequency carbonate chemistry observations from an Australian reef flat and simple numerical models, we show that TA–DIC slopes primarily reflect the temporal co‐variability of NEC and NEP, rather than their time‐integrated metabolic balance. To recover time‐integrated metabolic information, diel reef measurements must be coupled with offshore reference conditions, which anchor changes in TA and DIC to NEC : NEP ratios. We further demonstrate that metabolic balance shifts systematically over the diel cycle and depends on light, indicating that it is inherently dynamic rather than static. Together, our results highlight the need to distinguish metabolic co‐variability from metabolic ratios when interpreting carbonate chemistry data in coral reef and other dynamic aquatic ecosystems.

Predation is a significant source of mortality for many prey taxa, but predation strength may be determined by predator-prey body size, functional morphology or their combination. Here, we explore the relative contribution of predator-prey sizes and morphology in determining predation risk and density-dependent consumption rates for 5 decapod predators of juvenile crown-of-thorns starfish (CoTS; Acanthaster sp.), a corallivorous pest species common across the Indo-Pacific. We found generalisable patterns in the allometric scaling of predation risk among predator species, with declining consumption probability as juvenile CoTS size increased and predator size decreased. However, distinct predator claw characteristics explained 2 contrasting foraging styles that modified allometric predation windows and constrained attack rate and handling time estimates. Frequent CoTS injury and relatively low consumption rates (1.4-3.6 CoTS d(-1)) typified interactions with Portunidae species, whose sharp, weak claws are largely ineffective for consuming benthic prey. By contrast, the red decorator crab Schizophrys aspera (Majidae) consumed larger quantities of CoTS (16.8-22.1 CoTS d(-1)) across a broader range of prey sizes (1-14 mm), at least in part due to specialised spatulate claws that appear well-suited for handling benthic prey. Our results suggest that predator-induced CoTS mortality is strongest for juveniles < 5 mm when multiple predators are capable of total consumption, but CoTS vulnerability may be prolonged in the presence of S. aspera. Variation in the abundance of these 2 predator types may impact overall juvenile cohort success and the time to reach size refuges, with consequences for CoTS outbreaks.

Despite extensive research on the western Pacific crown-of-thorns starfish (CoTS; Acanthaster cf. solaris), especially from Australia’s Great Barrier Reef (GBR), there are persistent knowledge gaps that constrain understanding and management. Given renewed population irruptions of CoTS on the GBR, alongside escalating climate impacts and direct anthropogenic pressures, a quantitative assessment of knowledge gaps was undertaken to identify research priorities and guide future efforts. In this study, 27 experts independently scored 206 research questions across seven Themes and 39 topics, based on four different criteria (Knowledge gap, Feasibility, Urgency, and Applicability). These questions were ultimately rationalized into 170 distinct questions, with scores aggregated across merged questions. Management was the highest scoring Theme for Urgency, Applicability, and overall. All but six of the 20 top-ranked questions were from the Management Theme and mainly related to Culling and/ or Monitoring. Most questions (158 out of 170) also scored highly for Feasibility, suggesting that there are existing methods and technical capability available to advance the extensive and diverse range of research questions that were posed, if resources were made available. This quantitative assessment provides guidance on the prioritization of potential research that could improve management of CoTS populations to improve coral protection outcomes on the GBR. This study also suggests that there are limited constraints to undertaking necessary research to address many of the persistent knowledge gaps relating to CoTS.

Coral reefs are experiencing rapid transformation under interacting pressures of climate change, direct human impacts, and biological disturbance. Outbreaks of the corallivorous crown-of-thorns sea star (COTS; Acanthaster spp.) are major drivers of coral mortality. In parallel, coral population dynamics are increasingly intertwined with environmental change. This review synthesizes current understanding of pressures facing coral reefs in the Anthropocene and the ecological and physiological traits that underpin COTS success and outbreaks. These include (a) early life stages being far more resilient to warming and acidification compared with corals; (b) expansion of juvenile rubble habitat due to reef degradation and coral mortality, thereby enhancing juvenile survival; and (c) concentration of COTS feeding on surviving corals, intensifying degradation of imperiled reefs. The degraded reef hypothesis integrates life-history plasticity, ontogenetic diet shifts, trophic interactions, and ecosystem feedbacks to explain emerging outbreak paradigms and how climate stressors are reshaping COTS-coral predator-prey relationships, informing predictions of reef trajectories and management strategies.

On coral reefs, disturbances commonly generate legacy materials in the form of coral rubble. Rubble morphometrics and the diversity of organisms that bind rubble together can influence recovery trajectories. The quantification of rubble movement threshold velocities has been used to predict rubble bed stability, a precursor to binding. Yet empirical data on bind strength across environmental gradients are needed to inform predictions of whether bound rubble beds will experience routine bind breakage, and thus poor recovery, under varying hydrodynamic regimes. Over 18 mo, we tracked the strength of binding organisms that colonised experimental rubble pairs along environmental gradients on the Great Barrier Reef and used strength to estimate breakage velocity thresholds. The degree of contact between rubble pieces was a key determinant of bind strength, which increased over time and was weakest at inshore sheltered sites, driven by a high proportion of macroalgal binds. Bind strength was a direct reflection of the binding community, with the strongest binds by vermetid snails, bivalves, solitary ascidians, hard corals, and crustose coralline algae. For most offshore and inshore exposed sites, the threshold velocity required to break apart bound rubble increased from similar to 1 m s(-1) after 4 mo of stability and binding succession to similar to 3 m s(-1) by 18 mo, though these thresholds will vary with rubble morphology, arrangement and resulting interstitial spacing. These findings can be used in conjunction with time-series hydrodynamic data to predict the potential for disturbed rubble beds to recover and thus optimise the deployment of reef restoration interventions.

Variability in predator–prey interactions can modulate population dynamics with impacts scalable to entire ecosystems. As notorious corallivores, crown-of-thorns sea stars (CoTS; Acanthaster spp.) have caused extensive losses of coral habitat during unexplained population outbreaks across the Indo-Pacific. While predation of adult CoTS may help to suppress their outbreaks, it does not sufficiently explain their profound boom-bust dynamics and so remains equivocal. Factors influencing early postsettlement mortality are generally more impactful on population size, thus lower trophic interactions involving juvenile CoTS may better contribute to outbreak prevention. We evaluated the impact of key predatory decapods that interact with juvenile CoTS in their coral rubble nursery before they emerge as destructive corallivores. Decapod density was influenced by habitat complexity and varied regionally, inverse to spatial trends in CoTS outbreaks on the Great Barrier Reef. Using eDNA gut content analysis, we confirmed seven species (~12% of individuals) of wild-caught decapod, collected from two reefs separated by >1,000 km, as CoTS predators. Owing to spatial variation in predator abundance and community structure, we estimated potential (previous aquarium experiments) and realized (eDNA results here) rates of CoTS consumption were ~3-fold and ~1.6-fold lower, respectively, in outbreak hotspots. Through combination of field and molecular techniques, we demonstrated the appreciable impact of cryptic predators on early population success of this nuisance species, which expands our knowledge of CoTS outbreaks, pest species management, and reef conservation. Resolving predator–prey interactions at lower levels of the ecosystem can be crucial to understanding broader ecological outcomes.

Organismal symbioses are fundamental to biodiversity, evolution, and ecosystem functioning. On coral reefs, many decapod species have formed distinct epibiotic symbioses through decoration tendencies that enhance diet, camouflage, and defence. The red decorator crab, Schizophrys aspera (Majidae: Decapoda), has a broad Indo-Pacific distribution and is a successful predator of juvenile crown-of-thorns seastars (CoTS; Acanthaster sp.). However, little is known of the biology and decorating symbioses of S. aspera on the Great Barrier Reef (GBR), where CoTS pose ongoing management challenges. We characterised S. aspera and its epibiont community collected in coral rubble patches on the southern GBR. S. aspera predominantly used sponges (94 ± 1%; mean ± SE) in its decoration, with greater proportions of the carapace covered for juveniles (58 ± 5%) and females (46 ± 4%) compared to males (24 ± 4%). In short-term (8-d) experiments, S. aspera substantially reduced sponge (31%) and algal (47%) cover on rubble pieces, demonstrating its potential to alter sessile communities. The close association of S. aspera with sponges and algae likely reflects its diet and enhances camouflage and chemical defence in its coral rubble niche on the GBR. As sessile taxa are often noxious, we postulate that these symbioses may confer resilience of S. aspera to plancitoxins in its consumption of CoTS. Evaluating how epibiont diversity and biochemistry shape the habitat associations, distribution, and role of S. aspera as predator and prey may be important to understanding its ability to mediate CoTS densities on the GBR and elsewhere.

Gerromorpha Popov, 1971 is a fascinating and diverse insect lineage that evolved about 200 Mya to spend their entire life cycle on the air-water interface and have since colonized all types of aquatic habitats. The subfamily Halobatinae Bianchi, 1896 is particularly interesting because some species have adapted to life on the open ocean-a habitat where insects are very rarely found. Several attempts have been made to reconstruct the phylogenetic hypotheses of this subfamily, but the use of a few partial gene sequences recovered only a handful of well-supported relationships, thus limiting evolutionary inferences. Fortunately, the emergence of high-throughput sequencing technologies has enabled the recovery of more genetic markers for phylogenetic inference. We applied genome skimming to obtain mitochondrial and nuclear genes from low-coverage whole-genome sequencing of 85 specimens for reconstructing a well-supported phylogeny, with particular emphasis on Halobatinae. Our study confirmed that Metrocorini Matsuda, 1960, is paraphyletic, whereas Esakia Lundblad, 1933, and Ventidius Distant, 1910, are more closely related to Halobatini Bianchi, 1896, than Metrocoris Mayr, 1865, and Eurymetra Esaki, 1926. We also found that Ventidius is paraphyletic and in need of a taxonomic revision. Ancestral state reconstruction suggests that Halobatinae evolved progressively from limnic to coastal habitats, eventually attaining a marine lifestyle, especially in the genus Halobates Eschscholtz, 1822, where the oceanic lifestyle evolved thrice. Our results demonstrate that genome skimming is a powerful and straightforward approach to recover genetic loci for robust phylogenetic analysis in non-model insects. Graphical Abstract

Critical loss of habitat is the greatest threat to biodiversity, yet some species are inherently plastic to and may even benefit from changes in ecosystem states. The crown-of-thorns sea star (CoTS; Acanthaster spp.) may be one such organism. CoTS are large corallivores native to the tropical Indo-Pacific and in unexplained high densities, can adversely affect entire coral reefs. Proximal causes of CoTS outbreaks remain elusive, so this phenomenon remains a daunting and costly challenge for reef conservation and management. Amplifying anthropogenic impacts and new empirical data point to the degraded reef hypothesis to explain the episodic nature of CoTS population outbreaks. We posit that loss of live coral paradoxically benefits CoTS juveniles, which accumulate in their rubble nursery habitat before conditions trigger their pulsed emergence as coral-eaters. We review trait plasticity across the CoTS life cycle and present the degraded reef hypothesis in an integrative understanding of their propensity to outbreak.

One of the least understood trophic pathways on coral reefs is the linkage between highly productive cryptic motile invertebrates (herein: cryptofauna) and the predatory vertebrates that underpin reef fisheries. As cryptofauna are difficult to observe and quantify, particularly in coral rubble where they proliferate, the diets of invertivores that forage in rubble have largely been determined through relative gut content analyses. Without congruent quantification of prey diversity, biomass, and rates of predation specific to rubble, it remains challenging to develop models of productivity and energy transfer. We calculated bite rates of six wrasses (Labridae) and a goatfish (Mullidae) commonly found foraging in rubble, using in situ videography on a coral reef in Palau, Western Micronesia. Consumption rates (i.e. individuals consumed) and prey preferences were determined using tank-based feeding experiments, where individual fish were presented with a diverse rubble community characterised before and after 2 h feeding trials. The motile cryptofauna community and invertivore diet consisted predominantly of Arthropoda (83

The adult life stage of many species of sea cucumbers (Echinodermata: Holothuroidea) can be rather conspicuous on the seafloor. On the other hand, juvenile sea cucumbers are rarely observed in nature, largely owing to their small size and affinity with cryptic habitats. The juvenile life stage represents an important knowledge gap in the supply side ecology of holothuroid species, including data on habitat preferences, nursery grounds, growth rates, and age-size estimates, potentially limiting the success of conservation strategies. This chapter reviews available information on the biology and ecology of sea cucumber juveniles from coral reefs to temperate, polar, and deep-sea habitats. We characterize the juvenile life stage associated with the diverse reproductive strategies of holothuroids and synthesize records of juveniles from the wild to assess the ecological parameters that shape holothuroid ontogeny.

In a high CO2 world, coral reefs face a perilous future due to the multitude of co-occurring climate stressors. Climate change is causing sea-level rise, thermal stress, ocean acidification, and an increase in the intensity of storms with associated physical, hydromechanical, and hydrochemical impacts (Albright et al. 2016a; Cheal et al. 2017; Hoegh-Guldberg et al. 2017; Hughes et al. 2017a, 2017b, 2018; Putnam et al. 2017; Tebaldi et al. 2021; NOAA https://tinyurl.com/53z66rdj). Moreover, the rate and magnitude of change of these stressors are well beyond what modern reefs have evolved to cope with over geological timeframes (Pandolfi et al. 2011). Climate-driven warming and marine heatwaves have caused significant coral bleaching and mortality and in some cases, collapse of reef structures and associated communities on the Great Barrier Reef (GBR) and elsewhere (Hughes et al. 2017, 2018). Heatwaves, especially in combination with cyclones, are the climate change stressors of the utmost contemporary concern for the GBR. Accordingly, this iconic reef system has a very uncertain future.

Disturbances on coral reefs—which are increasing in intensity and frequency—generate material legacies. These are commonly in the form of rubble beds, which depend on rubble stability and/or binding to facilitate coral recruitment and recovery. Yet, our understanding of rubble stability and binding dynamics across environmental gradients is limited. Characterising and categorising rubble material legacies in context of their likely recovery trajectory is imperative to the effective deployment of active intervention strategies used to restore degraded reefs, such as rubble stabilisation, coral outplanting and larval seeding techniques. We quantified rubble characteristics across environmental gradients on the Great Barrier Reef. The likelihood of rubble stability and binding increased with rubble length and rubble bed thickness, and rubble length was a good predictor of bed thickness and rubble branchiness. Thin rubble bed profiles (< ~10 cm depth), those with small, unbranched rubble pieces (< ~10 cm length), and beds at the base of sloped rubble screes, had lower stability and binding likelihoods. These kinds of beds are expected to persist with low recovery prospects, and could be good candidates for rubble stabilisation interventions. Thicker rubble beds with larger, branched rubble pieces tended to exhibit higher stability and binding likelihoods. However, these beds had nuanced effects on coral cover, and interventions may still be necessary where competition is high, for example from macroalgae. A rapid assessment of rubble length—while also considering shelf location, geomorphic zone, slope angle and underlying substrate—can indicate the potential direction of a rubble bed's recovery trajectory. Our findings have been summarised into a rapid rubble bed assessment tool available in the Supporting Information, that can be incorporated into current reef monitoring to optimize prioritisation of intervention strategies at disturbed sites.

It has long been recognized that bioturbation and deposit-feeding activity by tropical holothuroids in the orders Holothuriida and Synallactida (Aspidochirotida s.l.) are among their primary ecological roles on coral reefs. The turnover of vast quantities of sediment through their feeding activities influences sedimentary properties including grain size, microalgal productivity, nutrient cycling, oxygen profiles, and biogeochemistry, with benefits to ecosystem functioning. Bioturbation and feeding processes, as well as site selectivity, resource partitioning, and thus species' distributions, vary among taxa, as do their potential contributions to sediment dissolution and biogenic buffering in a changing ocean. However, whether tropical holothuroids have an appreciable impact on their sedimentary biomes at regional scales remains a critical knowledge gap. This may be associated with the lack of data available on sea cucumbers before their widespread overharvest in the tropics. Thus, the ecological consequences of the exhaustive removal of holothuroids from coral reefs are discussed here in the context of their functional roles in tropical sedimentary biomes.

Patterns of movement of marine species can reflect strategies of reproduction and dispersal, species' interactions, trophodynamics, and susceptibility to change, and thus critically inform how we manage populations and ecosystems. On coral reefs, the density and diversity of metazoan taxa are greatest in dead coral and rubble, which are suggested to fuel food webs from the bottom up. Yet, biomass and secondary productivity in rubble is predominantly available in some of the smallest individuals, limiting how accessible this energy is to higher trophic levels. We address the bioavailability of motile coral reef cryptofauna based on small-scale patterns of emigration in rubble. We deployed modified RUbble Biodiversity Samplers (RUBS) and emergence traps in a shallow rubble patch at Heron Island, Great Barrier Reef, to detect community-level differences in the directional influx of motile cryptofauna under five habitat accessibility regimes. The mean density (0.13-4.5 ind cm-3) and biomass (0.14-5.2 mg cm-3) of cryptofauna were high and varied depending on microhabitat accessibility. Emergent zooplankton represented a distinct community (dominated by the Appendicularia and Calanoida) with the lowest density and biomass, indicating constraints on nocturnal resource availability. Mean cryptofauna density and biomass were greatest when interstitial access within rubble was blocked, driven by the rapid proliferation of small harpacticoid copepods from the rubble surface, leading to trophic simplification. Individuals with high biomass (e.g., decapods, gobies, and echinoderms) were greatest when interstitial access within rubble was unrestricted. Treatments with a closed rubble surface did not differ from those completely open, suggesting that top-down predation does not diminish rubble-derived resources. Our results show that conspecific cues and species' interactions (e.g., competition and predation) within rubble are most critical in shaping ecological outcomes within the cryptobiome. These findings have implications for prey accessibility through trophic and community size structuring in rubble, which may become increasingly relevant as benthic reef complexity shifts in the Anthropocene.

Crown-of-thorns starfish (CoTS) are a pervasive coral predator prone to population outbreaks that have damaged coral reefs across Australia and the wider Indo-Pacific. CoTS population control through predation has been suggested as a primary mechanism that suppresses their outbreaks. However, the nature and rates of predation on CoTS are poorly resolved, especially for early life-history stages where they are expected to be most vulnerable. Here, we provide results from the first investigation of predators of CoTS during their rubble-dwelling, herbivorous, juvenile phase. We assessed the capacity of 104 common species of the rubble cryptofauna found across Heron Reef, Great Barrier Reef, Australia, to consume early-stage juvenile CoTS (0.8–3.8 mm) using controlled feeding experiments with laboratory-raised juveniles. We identified 26 novel CoTS predators, but only 10 species that regularly consumed juvenile CoTS in their entirety. Most cases of predation resulted in severed bodies and missing arms (i.e. sublethal predation) but not total consumption. We highlight one crustacean predator, Schizophrys aspera , the red decorator crab, which consumed whole juvenile CoTS in 89% of feeding trials and in excess of 5 CoTS d −1 in natural rubble mesocosms with alternative prey. This work emphasises the importance of predators at the critical juvenile stage that may control the build-up of CoTS populations prior to being detectable as an outbreak population.

With rubble predicted to increase on coral reefs worldwide, we review the physical, biological, and ecological dynamics of rubble beds, with a focus on how rubble generation, mobilization, binding, and coral recruitment is expected to change on future reefs. Major disturbances, including storms and coral bleaching, are predicted to increase in intensity and frequency, and-like localized impacts including blast fishing and ship groundings-generate large quantities of coral rubble. Reefs will have increasingly smaller recovery windows between successive disturbances, leading to persistence of unstable rubble beds on reefs. With more severe storms and increased bioerosion on future reefs, rubble mobilization thresholds will be met more often as smaller, less complex rubble pieces are generated. If rubble remains stable for adequate time, it can be bound by organisms including sponges and coralline algae, and eventually be cemented. However, increasing rubble mobilization frequencies will reduce the time available for binding, while changing ocean chemistry could reduce the efficacy of calcifying binders. Ultimately, increased rubble cover will negatively impact coral recruitment into rubble beds. Rubble mobilization abrades and smothers corals, and rubble beds typically experience altered environmental and ecological conditions to the coral frameworks that precede them. Several knowledge gaps exist in relation to improved rubble mobilization thresholds, binding rates and strengths, and coral survival in varying rubble bed types and hydrodynamic regimes. Addressing these knowledge gaps will improve our ability to predict the recovery trajectory of rubble beds and assess the need for stabilization interventions.

Declines in habitat structural complexity have marked ecological outcomes, as currently observed in many of the world's ecosystems. Coral reefs have provided a model for such changes in marine ecosystems; still our understanding has been centered on corals and fishes at broad spatial scales when metazoan diversity on coral reefs is dominated by small cryptic taxa (herein: "cryptofauna"). Given the paucity of studies and high taxonomic complexity of the cryptofauna, both of which limit a priori hypotheses, we asked whether hierarchical structuring theory provides a compelling framework to impose order and quantify patterns. In general terms, we explored whether cryptic communities are sufficiently described by broad seascape parameters or limited by a set of processes operating at their distinctly nested microhabitat scale. To address this theory and gaps in knowledge for the cryptofauna, we characterized community structure in coral rubble, an eroded coral condition where biodiversity proliferates. Rubble was sampled along a depth and exposure gradient at Heron Island on the Great Barrier Reef, Australia, to parameterize environmental and morphological indicators of sessile taxa and motile cryptofauna communities. We used a hierarchical study framework from microhabitat to seascape scales, which were evaluated using nonstructured multivariate analyses and Bayesian structural equation modeling. While the nonstructured analyses showed the effects of seascape on the cryptobenthos and its community, this approach overlooked the finer hierarchical patterns in rubble ecology revealed only in the structured model. Seascape parameters (exposure and depth) influenced microhabitat complexity (i.e., rubble branchiness), which determined the cover of sessile organisms on rubble pieces, which shaped the motile cryptofauna community. Rubble is likely to be increasingly prevalent on coral reefs in the Anthropocene and is typically associated with low seascape-level complexity and reduced macrofaunal richness. Parallel with hierarchical structuring theory, we showed a similar response operating at the microhabitat scale whereby low rubble complexity (i.e., branchiness) reduced cryptobenthic structure, diversity and size spectra. In a future ocean, we expect there may be an initial increase in biodiversity and trophodynamic processes derived from branching rubble, but a delay in ecosystem-scale outcomes if coral, and thus rubble, generation and complexity is not sustained.

Cryptic species and their interactions are challenging to describe owing to the difficulties in observing and sampling their populations. Such methodological hurdles are critical to resolve, especially when important interactions involving poorly described species are detected. The red decorator crab, Schizophrys aspera, is a newfound predator of the corallivorous Pacific crown-of-thorns seastar (CoTS; Acanthaster sp.). We discuss the Indo-Pacific distribution and taxonomy of S. aspera and provide characterization of its cryptic population at sites around Heron Island, Great Barrier Reef, that differ in CoTS densities. Most S. aspera (>95%) were found under coral rubble pieces atop existing rubble, associated with large pieces and chasmic interstices. The three smallest individuals (carapace width: 5-11 mm) were found under rubble overlying sand. Mean density of S. aspera was 0.8 +/- 0.2 ind. 100 m(-2), which varied among sites. Areas with lower records of CoTS had higher densities of S. aspera (p = 0.002; R-2 = 0.25), which justifies evaluation of the distribution and impact of this species in context of CoTS outbreaks. We present a method to survey cryptic decapods on coral reefs, along with microhabitat characteristics to help predict S. aspera on reefs prone to CoTS outbreaks and its capacity to act as a natural top-down control mechanism.