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Marine sponges have recently been recognized as natural samplers of environmental DNA (eDNA) due to their effective water filtration and their ubiquitous, sessile, and regenerative nature. However, laboratory workflows for metabarcoding of sponge tissue have not been optimized to ensure that these natural samplers achieve their full potential for community survey. We used a phased approach to investigate the influence of DNA isolation procedures on the biodiversity information recovered from sponges. In Phase 1, we compared three treatments of residual ethanol preservative in sponge tissue alongside five DNA extraction protocols. The results of Phase 1 informed which ethanol treatment and DNA extraction protocol should be used in Phase 2, where we assessed the effect of starting tissue mass on extraction success and whether homogenization of sponge tissue is required. Phase 1 results indicated that ethanol preservative may contain unique and/or additional biodiversity information to that present in sponge tissue, but blotting tissue dry generally recovered more taxa and generated more sequence reads from the wild sponge species. Tissue extraction protocols performed best in terms of DNA concentration, taxon richness, and proportional read counts, but the non-commercial tissue protocol was selected for Phase 2 due to cost-efficiency and greater recovery of target taxa. In Phase 2 overall, we found that homogenization may not be required for sponge tissue and more starting material does not necessarily improve taxon detection. These results combined provide an optimized DNA isolation procedure for sponges to enhance marine biodiversity assessment using natural sampler DNA metabarcoding., This study was funded by the UK Natural Environment Research Council grant NE/T007028/1. A.R. was also supported by the Spanish Ministry of Science and Innovation grant (RYC2018-024247-I) and CSIC intramural grant (202030E006). M.B.A. was supported by the National Agency for Research and Development (ANID), fellowship program Postdoctorado en el extranjero/2019-74200143.

Reef-building corals owe their evolutionary success to their symbiosis with unicellular algae (Symbiodiniaceae). However, increasingly frequent heat waves lead to coral mass-bleaching events and pose a serious threat to the survival of reef ecosystems. Despite significant efforts, a mechanistic understanding of coral–algal symbiosis functioning, what leads to its breakdown and what can prevent it, remains incomplete. The main obstacles are low amenability of corals to experimental handling and, owing to its obligatory nature, the difficulties of manipulating the coral–algal association. Indeed, many studies on the symbiotic partnership are conducted on other cnidarian model organisms and their results may therefore not be fully transferable to tropical reef-building corals. Here, we identify the tropical stony coral species Galaxea fascicularis as a novel candidate coral model system. Individual polyps of this species can be separated, enabling highly replicated genotype studies, and are well suited to experimental investigation of the symbiosis as they can be easily and effectively rid of their algal symbionts (bleached). We show that bleached adult individuals can reestablish symbiosis with non-native symbionts, and we report the completion of the gametogenic cycle ex situ, with the successful spawning in aquaria over multiple years. These achievements help overcome several of the major limitations to direct research on corals and highlight the potential of G. fascicularis as an important new model system for investigations of symbiosis functioning and manipulation.

The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential “single observer” effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion. Supplementary Information The online version contains supplementary material available at 10.1007/s12686-021-01250-3.

Larval dispersal is critical to the survival of coral reefs. As the only motile stage of the reproductive cycle, coral larvae choose a suitable location to settle and mature into adult corals. Here, we present the first detailed study of ciliary propulsion in the common stony reef coral Acropora millepora. Using high-speed, high-resolution imaging, particle image velocimetry, and electron microscopy, we reveal the arrangement of the densely packed cilia over the larval body surface, and their organisation into diaplectic (transversely propagating) metachronal waves. We resolve the individual-cilium’s beat dynamics and compare the resultant flows with a computational model of a ciliary array, and show that this form of ciliary metachronism leads to near-maximal pumping efficiency.

Reef-building corals owe their evolutionary success to their symbiosis with unicellular algae (Symbiodiniaceae). However, increasingly frequent heat waves lead to coral mass-bleaching events and pose a serious threat to the survival of reef ecosystems. Despite significant efforts, a mechanistic understanding of coral-algal symbiosis functioning, what leads to its breakdown and what can prevent it, remains incomplete. The main obstacles are low amenability of corals to experimental handling and, owing to its obligatory nature, the difficulties of manipulating the coral-algal association. Indeed, many studies on the symbiotic partnership are conducted on other cnidarian model organisms and their results may therefore not be fully transferable to tropical reef-building corals. Here, we identify the tropical stony coral speciesGalaxea fascicularisas a novel candidate coral model system. Individual polyps of this species can be separated, enabling highly replicated genotype studies, and are well suited to experimental investigation of the symbiosis as they can be easily and effectively rid of their algal symbionts (bleached). We show that bleached adult individuals can reestablish symbiosis with non-native symbionts, and we report the completion of the gametogenic cycleex-situ, with the successful spawning in aquaria over multiple years. These achievements help overcome several of the major limitations to direct research on corals and highlight the potential ofG. fascicularisas an important new model system for investigations of symbiosis functioning and manipulation.

Studies of broadcast spawning in corals are fundamental to our understanding of early life history characteristics, reproductive biology, restoration etc. Spawning of corals for research is routine...

Members of the family Meandrinidae are highly susceptible to stony coral tissue loss disease, resulting in population reductions up to 88% in both Dendrogyra cylindrus and Meandrina meandrites along the Florida Reef Tract. Reductions in abundance on this scale leave these species susceptible to limitations in sexual reproduction and natural recovery without intervention. In response to the ongoing outbreak of the disease across the Caribbean, a variety of genetic rescue projects have been implemented to bring disease susceptible species into ex situ culture and preserve living genetic diversity. In this study, corals being held in a long-term ex situ genetic bank were maintained using artificial lighting and temperature cues programmed to mimic natural cycles in Key Largo, FL, United States. Synchronized broadcast spawning events in both species were documented in aquaria over two annual spawning cycles in 2019 and 2020. Timing of gamete release relative to the perceived date and sunset was highly synchronized with wild observations. Up to 21 unique D. cylindrus genotypes collected from reef locations spanning over 230 km contributed gametes to the larval pool. The majority of these parental colonies are no longer alive in the wild. Repeatable and predictable ex situ spawning events such as these will become an essential tool for managed breeding and assisted fertilization in species suffering from severe population declines. These annual events have the potential to produce thousands of genetically diverse offspring for restoration efforts and offer future hope for the long-term survival of these threatened species.

Coral reefs are suffering unprecedented declines in health state on a global scale. Some have suggested that human assisted evolution or assisted gene flow may now be necessary to effectively restore reefs and pre-condition them for future climate change. An understanding of the key metabolic processes in corals, including under stressed conditions, would greatly facilitate the effective application of such interventions. To date, however, there has been little research on corals at this level, particularly regarding studies of the metabolome of Scleractinian corals. Here, the metabolomic profiles [measured using 1H nuclear magnetic resonance spectroscopy (1H NMR) and ultra-high-performance liquid chromatography-mass spectrometry (LC-MS)] of two dominant reef building corals, Acropora hyacinthus and A. millepora, from two distinct geographical locations (Australia and Singapore) were characterized. We assessed how an acute temperature stress (an increase of 3.25°C ± 0.28 from ambient control levels over 8 days), shifted the corals’ baseline metabolomic profiles. Regardless of the profiling method utilized, metabolomic signatures of coral colonies were significantly distinct between coral species, a result supporting previous work. However, this strong species-specific metabolomic signature appeared to mask any changes resulting from the acute heat stress. On closer examination, we were able to discriminate between control and temperature stressed groups using a partial least squares discriminant analysis classification model (PLSDA). However, in all cases “late” components needed to be selected (i.e., 7 and 8 instead of 1 and 2), suggesting any treatment effect was small, relative to other sources of variation. This highlights the importance of pre-characterizing the coral colony metabolomes, and of factoring that knowledge into any experimental design that seeks to understand the apparently subtle metabolic effects of acute heat stress on adult corals. Further research is therefore needed to decouple these apparent individual and species-level metabolomic responses to climate change in corals.

Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches, such as selective breeding for adaptive traits combined with large-scale sexual propagation, are being developed with the aim of pre-adapting reefs to increased ocean warming. However, there are still major gaps in our understanding of the technical and methodological constraints to producing corals for such restoration interventions. Here we propose a framework for selectively breeding corals and rearing them from eggs to 2.5-year old colonies using the coral Acropora digitifera as a model species. We present methods for choosing colonies for selective crossing, enhancing early survivorship in ex situ and in situ nurseries, and outplanting and monitoring colonies on natal reefs. We used a short-term (7-day) temperature stress assay to select parental colonies based on heat tolerance of excised branches. From six parental colonies, we produced 12 distinct crosses, and compared survivorship and growth of colonies transferred to in situ nurseries or outplanted to the reef at different ages. We demonstrate that selectively breeding and rearing coral colonies is technically feasible at small scales and could be upscaled as part of restorative assisted evolution initiatives. Nonetheless, there are still challenges to overcome before selective breeding can be implemented as a viable conservation tool, especially at the post-settlement and outplanting phases. Although interdisciplinary approaches will be needed to overcome many of the challenges identified in this study, selective breeding has the potential to be a viable tool within reef managers’ toolbox to support the persistence of selected reefs in the face of climate change.

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.

Reef restoration efforts, utilising sexual coral propagation need up-scaling to have ecologically meaningful impact. Post-settlement survival bottlenecks, in part due to competitive benthic algae interactions should be addressed, to improve productivity for these initiatives. Sea urchins are keystone grazers in reef ecosystems, yet feeding behaviour of adults causes physical damage and mortality to developing coral spat. To investigate if microherbivory can be utilised for co-culture, we quantitatively assessed how varying densities of juvenile sea urchins Mespilia globulus (Linnaeus, 1758), reared alongside the coral Acropora millepora (Ehrenberg, 1834) effected survival and growth of coral recruits. Spawning of both species were induced ex situ. A comparison of A. millepora spat reared in three M. globulus densities (low 16.67 m−2, medium 37.50 m−2, high 75.00 m−2) and a non-grazed control indicated coral survival is significantly influenced by grazing activity (p p

The influence of copepod prey size and behaviour upon Aurelia aurita medusae predation rates was investigated. There was no significant difference in predation rates across a 4-fold (250 to 987 mm) prey size range (heat-killed developmental stages of Acartia tonsa). Any behavioural differences (e.g. swimming speed, escape response) across live A. tonsa developmental stages had no significant effect upon their susceptibility to predation. In addition, Aurelia aurita ingestion rates were similar upon adult males and females of a copepod that exhibit similar swimming speeds (A. tonsa), as well as upon both adult sexes of a copepod with contrasting swimming behaviour (Oithona similis). An encounter model indicated that the size and speed of Aurelia aurita overwhelmed the differences in size and swimming speeds of these prey by largely determining encounter rates. However, overall, heat-killing prey lead to significantly higher predation rates than those upon live prey. This may be attributed to the escape response of live prey, which is not included in the encounter model. The capture efficiency of Aurelia aurita was low (,9%), but high ingestion rates may be achieved through the large encounter rates of this cruising predator.

In order to quantify the trophic impact of gelatinous predators, digestion time estimates are commonly applied to counts of prey in the guts. Three primary approaches are used, the Manual-feeding, Natural-feeding and Steady-state methods; these differ in methodology and their underlying assumptions. The criteria used to define the end-point of digestion, and the resolution at which digestion progress is observed, also vary across studies. To understand the impact of such differences, we estimate digestion times of the scyphomedusa Aurelia aurita fed adult females of the copepod Acartia tonsa using these various approaches. We find ~fourfold differences which can be attributed to bias towards the slowest rates of digestion by some end-point criteria, and overestimation from low observation resolution. Artificial manipulation and the degree to which swimming and feeding behaviour are natural may also influence estimates. We provide recommendations for those quantifying digestion times of Aurelia aurita medusae and gelatinous predators.

The effect of increased levels of suspended sediment on fertilization success in the scleractinian coral Pectinia lactuca was investigated in a laboratory experiment following a mass coral spawning event on reefs off Singapore. Egg–sperm bundles were collected from tank-spawned coral colonies collected from the field several days prior to the anticipated mass spawning. Eggs and sperm from each colony were separated and distributed systematically across replicated treatments (N = 9) with three concentrations of fine suspended sediment. Spawning and embryo development in Pectinia lactuca followed a pattern similar to other scleractinian coral species. There was a significant effect of increased suspended sediment concentration on fertilization success (P −1) and medium- (43 mg l−1) suspended sediment treatments decreased fertilization success compared to controls. These results imply that increased turbidity levels (whether chronic, such as in the waters around Singapore, or short-term, caused by a dredging operation)—when coinciding with the coral spawning season—may affect the reproductive success of corals and compromise coral recruitment and recovery of degraded reefs.

Large and hyperdiverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as “natural samplers” of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the dynamics of eDNA particles in sponge tissue, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA captured by three encrusting sponge species and compare the sponge's eDNA capturing ability with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the “chosen” natural samplers in certain habitats and regions., This study was supported by grant NE/T007028/1 from the UK Natural Environment Research Council. A.R. was also supported by the Spanish Ministry of Science and Innovation grant (RYC2018-024247-I) and CSIC intramural grant (202030E006).