Large‐scale coral reef rehabilitation after blast fishing in Indonesia

The severely degraded condition of many coral reefs worldwide calls for active interventions to rehabilitate their physical and biological structure and function, in addition to effective management of fisheries and no‐take reserves. Rehabilitation efforts to stabilize reef substratum sufficiently to support coral growth have been limited in size. We documented a large coral reef rehabilitation in Indonesia aiming to restore ecosystem functions by increasing live coral cover on a reef severely damaged by blast fishing and coral mining. The project deployed small, modular, open structures to stabilize rubble and to support transplanted coral fragments. Between 2013 to 2015, approximately 11,000 structures covering 7,000 m² were deployed over 2 ha of a reef at a cost of US$174,000. Live coral cover on the structures increased from less than 10% initially to greater than 60% depending on depth, deployment date and location, and disturbances. The mean live coral cover in the rehabilitation area in October 2017 was higher than reported for reefs in many other areas in the Coral Triangle, including marine protected areas, but lower than in the no‐take reference reef. At least 42 coral species were observed growing on the structures. Surprisingly, during the massive coral bleaching in other regions during the 2014–2016 El Niño–Southern Oscillation event, bleaching in the rehabilitation area was less than 5% cover despite warm water (≥30°C). This project demonstrates that coral rehabilitation is achievable over large scales where coral reefs have been severely damaged and are under continuous anthropogenic disturbances in warming waters.     

Enhancing coral larval supply and seedling production using a special bundle collection system “coral larval cradle” for large‐scale coral restoration

Larval recruitment is essential for sustaining coral communities and a fundamental tool in some interventions for reef restoration. To improve larval supply and post‐settlement survival in sexually assisted coral restoration efforts, an integrated in situ collector system, the larval cradle, was designed to collect spawned gametes then culture the resulting larvae until settled on artificial substrates. The final design of the larval cradle was cylindrical, a nylon mesh structure with a volume of 9 m³, suspended in the sea and extending vertically toward the seabed. We found three key design features that improved the efficiency of the apparatus: (1) an open area of sea surface and mesh size of less than 100 μm produced high fertilization and optimal survival (>90%), (2) a special skirt‐shaped net (3 m in diameter) with a connection hose for attaching the cradle to collect bundles from many adult colonies over a wide area and at various depths, and (3) adding short square tube pieces, called square hollow sections, as a substrate for enhancing larval settlement and survival, to a larval cradle at 4 days after spawning was optimal for uniform settlement. This system allowed not only the collection of several million eggs, but also subsequent production of several thousand settled juvenile corals, without land facilities. Our design achieved several hundred times higher survival for early life stages of Acropora tenuis compared to nature.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Coral reefs modify their seawater carbon chemistry – case study from a barrier reef (Moorea,French Polynesia)

Changes in the carbonate chemistry of coral reef waters are driven by carbon fluxes from two sources: concentrations of CO₂ in the atmospheric and source water, and the primary production/respiration and calcification/dissolution of the benthic community. Recent model analyses have shown that, depending on the composition of the reef community, the air‐sea flux of CO₂ driven by benthic community processes can exceed that due to increases in atmospheric CO₂ (ocean acidification). We field test this model and examine the role of three key members of benthic reef communities in modifying the chemistry of the ocean source water: corals, macroalgae, and sand. Building on data from previous carbon flux studies along a reef‐flat transect in Moorea (French Polynesia), we illustrate that the drawdown of total dissolved inorganic carbon (C_T) due to photosynthesis and calcification of reef communities can exceed the draw down of total alkalinity (A_T) due to calcification of corals and calcifying algae, leading to a net increase in aragonite saturation state (Ω_a). We use the model to test how changes in atmospheric CO₂ forcing and benthic community structure affect the overall calcification rates on the reef flat. Results show that between the preindustrial period and 1992, ocean acidification caused reef flat calcification rates to decline by an estimated 15%, but loss of coral cover caused calcification rates to decline by at least three times that amount. The results also show that the upstream–downstream patterns of carbonate chemistry were affected by the spatial patterns of benthic community structure. Changes in the ratio of photosynthesis to calcification can thus partially compensate for ocean acidification, at least on shallow reef flats. With no change in benthic community structure, however, ocean acidification depressed net calcification of the reef flat consistent with findings of previous studies.     

Coralclip®: a low‐cost solution for rapid and targeted out‐planting of coral at scale

Re‐attaching or out‐planting coral as fragments, colonies, and on larval settlement devices to substrates is a major bottleneck limiting scalabilty and viability of reef restoration practices. Many attachment approaches are in use, but none that are low‐cost, opportunistic, rapid but effective, for integration into existing tour operations on the Great Barrier Reef (GBR) where staff and boat time is a major cost and chemical fixatives cannot be easily used. We describe a novel attachment device—Coralclip®—developed to meet this need and so aid maintenance and restoration of GBR tourism sites. Coralclip® is a stainless steel springclip attached by a nail integrated through the spring coil, and can be deployed with a coral fragment in as fast as 15 seconds. Initial laboratory tests demonstrated that Coralclip® secured coral fragments or larval settlement tiles under dynamic flow regimes characteristic of exposed reefs. Coral out‐planting from fragments of opportunity and from nurseries (n = 4,580; 0.3–1.9 coral/minute; US$0.6–3.0/coral deployed) or larval settlement tiles (n = 400; 2.5 tiles/minute; US$0.5 tile deployed^?1) when deployed by divers from routine boat operations at Opal Reef confirmed highly effective attachment, with ≤15% failure of clips found after 3–7 months. We discuss how Coralclip® is a cost‐effective means to support reef maintenance and restoration practices.     

Cycles of coral reef ‘turn‐on’, rapid growth and ‘turn‐off’ over the past 8500 years: a context for understanding modern ecological states and trajectories

Human activities threaten reef ecosystems globally, forcing ecological change at rates and scales regarded as unprecedented in the Holocene. These changes are so profound that a cessation of reef accretion (reef ‘turn‐off’) and net erosion of reef structures is argued by many as the ultimate and imminent trajectory. Here, we use a regional scale reef growth dataset, based on 76 core records (constrained by 211 radiometric dates) from 22 reefs along and across the inner‐shelf of the Great Barrier Reef, Australia, to examine the timing of different phases of reef initiation (‘turn‐on’), growth and ‘turn‐off’ during the Holocene. This dataset delineates two temporally discrete episodes of reef‐building over the last 8500 years: the first associated with the Holocene transgression‐early highstand period [～8.5–5.5 k calibrated years bp (cal ybp )]; the second since ～2.3 k cal ybp . During both periods, reefs accreted rapidly to sea level before entering late evolutionary states – states naturally characterized by reduced coral cover and low accretion potential – and a clear hiatus occurs between these reef‐building episodes for which no records of reef initiation exist. These transitions mimic those projected under current environmental disturbance regimes, but have been driven entirely by natural forcing factors. Our results demonstrate that, even through the late Holocene, reef health and growth has fluctuated through cycles independent of anthropogenic forcing. Consequently, degraded reef states cannot de facto be considered to automatically reflect increased anthropogenic stress. Indeed, in many cases degraded or nonaccreting reef communities may reflect past reef growth histories (as dictated by reef growth–sea level interactions) as much as contemporary environmental change. Recognizing when changes in reef condition reflect these natural ‘turn‐on’– growth –‘turn‐off’ cycles and how they interact with on‐going human disturbance is critical for effective coral reef management and for understanding future reef ecological trajectories.     

Leucothoe eltoni sp. n., a new species of commensal leucothoid amphipod from coral reefs in Raja Ampat,Indonesia (Crustacea,Amphipoda)

A new species of leucothoid amphipod, Leucothoeeltoni sp. n., is described from coral reefs in Raja Ampat, Indonesia where it inhabits the branchial chambers of solitary tunicates. With an inflated first gnathopod superficially resembling the genus Paraleucothoe, this new species has a two-articulate maxilla 1 palp characteristic of the genus Leucothoe. While described from coral reef environments in tropical Indonesia and the Philippines, it is an established invasive species in the Hawaiian Islands. The most likely mode of introduction was a US Navy dry dock transported to Pearl Harbor in 1992 from Subic Bay, Philippines.     

Recognition of separate genera within Acropora based on new morphological, reproductive and genetic evidence from Acropora togianensis , and elevation of the subgenus Isopora Studer, 1878 to genus (Scleractinia: Astrocoeniidae; Acroporidae)

Many attempts have been made to recognise divisions within Acropora, the most diverse reef building coral genus on modern reefs, but only subgenera Acropora and Isopora are currently recognised. In this paper, morphological and genetic analyses, and study of reproductive mode and anatomy, demonstrate that an endemic Indonesian species A. (Acropora) togianensis, Wallace, 1997, belongs to Isopora. Despite the presence of a clear central axial corallite (indicating sub-genus Acropora), this species has supplementary axial corallites, broods planula larvae rather than broadcast-spawning for external fertilisation and develops stalked ova: all characters in common with the type species of subgenus Isopora A. (Isopora) palifera and the other species for which such data are available, A. (I.) cuneata and A. (I.) brueggemanni. Phylogenies are based on the protein-coding genes, mitochondrial cytochrome b (cytb) and nuclear histone 2a and 2b (h2ab) also group A. togianensis with these Isoporans. High bootstrapping and Bayesian support in the major lineages of the family Acroporidae demonstrate significant differences between Isopora (including A. togianensis) and Acropora. As the type species of both subgenera, A. (Acropora) muricata (Linneaus 1758) and A. (Isopora) palifera (Lamarck, 1816) are used in these analyses, elevation of Isopora Studer, 1878 to genus is formally proposed.     

Effects of coral restoration on fish communities: snapshots of long‐term,multiregional responses and implications for practice

Coral restoration is widely used around the world to address dramatic declines in coral cover; however, very few studies have looked specifically at the temporal response of fish assemblages (i.e. abundance and diversity) to coral restoration. Several critical reef functions and processes are driven by fishes, thereby making their recovery and responses around restoration structures key indicators of success. This study evaluates fish abundance and community composition on restoration plots following 8–12 years of restoration activity, in four locations (two Caribbean and two Indo‐Pacific). Responses were very complex with region‐, site‐, and body size‐specific patterns. Overall, fish abundance only increased in Indo‐Pacific sites where damselfish responded positively to increased coral cover and topographic complexity. Restoration effects on other fish families and particularly on larger bodied reef fish were negative or neutral at all locations. If restoration initiatives are going to substantively improve the condition and recovery of degraded reef fish communities, restoration efforts need to be planned, designed, and monitored based on fish‐specific habitat requirements and locally specific community dynamics.     

Climate change and coral reefs: different effects in two high-latitude areas (Arabian Gulf,South Africa)

The findings in this paper show that Arabian Gulf (Abu Dhabi, Dubai, Sharjah) corals have already been measurably affected by climate change and further negative impacts are expected. Corals in South Africa have been only weakly impacted and are expected to persist in this likely refuge. The Arabian Gulf has recently experienced high-frequency recurrences of temperature-related bleaching (1996, 1998, 2002). First evidence may suggest that bleaching patterns in corals changed due to phenotypic adaptation after two strong bleaching events in rapid succession, because Acropora, which during the 1996 and 1998 events always bleached first and suffered heaviest mortality, bleached less than all other corals in 2002 at Sir Abu Nuair and recovered at Jebel Ali and Ras Hasyan. In South Africa, reef corals largely escaped the mass mortalities observed across the tropics in the late 1990s, although bleaching has also increased since 1999. These reefs are protected by local small-scale upwelling events in summer that, if they occur at the right time, keep temperatures below bleaching levels. Both areas, the Arabian Gulf and South Africa, have rich coral faunas but little to no recent reef-framework production. It is possible that many reefs worldwide may have similar dynamics in the future, if the changed climate (recurrence of temperature anomalies, changes in aragonite saturation state, etc.) suppresses sustained reef building at least temporarily. Global climate models predict the possibility of significant environmental changes, including increases in atmospheric temperature, sea-surface temperature (SST), and sea level. Monsoon and El Niño Southeastern Oscillation (ENSO) patterns might change, but climate models are not conclusive. Sea-level rise by up to 0.88 m is expected to be a problem in some low-lying areas, like the southern Arabian Gulf. Ocean aragonite saturation state is predicted to fall throughout the ocean but may not change reef dynamics in the two study areas.     

Genomic signatures of host‐associated divergence and adaptation in a coral‐eating snail,Coralliophila violacea (Kiener, 1836)

The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo‐Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails’ adaptation to their coral hosts. Genome‐wide single nucleotide polymorphism (SNP) data from type II restriction site‐associated DNA (2b‐RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host‐associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N. kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns

The maskray from New Caledonia, Neotrygon trigonoides Castelnau, 1873, has been recently synonymized with the blue-spotted maskray, N. kuhlii (Müller and Henle, 1841), a species with wide Indo-West Pacific distribution, but the reasons for this are unclear. Blue-spotted maskray specimens were collected from the Indian Ocean (Tanzania, Sumatra) and the Coral Triangle (Indonesia, Taiwan, and West Papua), and N. trigonoides specimens were collected from New Caledonia (Coral-Sea). Their partial COI gene sequences were generated to expand the available DNA-barcode database on this species, which currently comprises homologous sequences from Ningaloo Reef, the Coral Triangle and the Great Barrier Reef (Coral-Sea). Spotting patterns were also compared across regions. Haplotypes from the Coral-Sea formed a haplogroup phylogenetically distinct from all other haplotypes sampled in the Indo-West Pacific. No clear-cut geographic composition relative to DNA-barcodes or spotting patterns was apparent in N. kuhlii samples across the Indian Ocean and the Coral Triangle. The New Caledonian maskray had spotting patterns markedly different from all the other samples. This, added to a substantial level of net nucleotide divergence (2.6%) with typical N. kuhlii justifies considering the New Caledonian maskray as a separate species, for which we propose to resurrect the name Neotrygon trigonoides.     

Distribution pattern, population structure, and growth of Septifer bilocularis (Bivalvia: Mytilidae) on reefs of Southern Vietnam

The features of the spatial distribution, size and age structure of populations, and growth of the bivalve mollusk Septifer bilocularis (Linnaeus, 1758) were investigated for the first time in the waters of Vietnam. It is shown that in the subtidal area, on reefs well protected from wave effects, S. bilocularis occupies a corallogenous substrate constructed of dead branchy colonies of Acropora and Porites and forms settlements there with a population density and biomass exceeding those in populations located along the open coast and developing on massive coral colonies of the genera Porites, Favia, and Favites. The extensive accumulation of sediments in the inner part of Vanphong Bay (Khanh Hoa Province) correlated with a decrease in the size and age ranges for populations of S. bilocularis. It is found that in places with regularly active hydrodynamics the mollusks grew somewhat more slowly and formed a more convex shell than on reefs protected from surf. The longevity of S. bilocularis estimated both from the greatest observed age and from the growth equation of Bertalanffy was somewhat greater in the former case compared with the latter one, but in general did not exceed 11 years for both cases. The results of the studies are discussed from the position of morphophysiological adaptations of sessile bivalve mollusks to life in contrasting environmental conditions of the upper subtidal zone.     

Spatial and size-frequency distribution of <Emphasis Type="Italic">Acropora</Emphasis> (Cnidaria: Scleractinia) species in Chinchorro Bank,Mexican Caribbean: implications for management

The Mexican Government decreed Chinchorro Bank reef as a Biosphere Reserve in 1996. The aim of this study was to evaluate the spatial and size-frequency distribution of Acropora spp. in order to provide further knowledge and tools to enhance management. A field survey was conducted, within six regions, to locate and measure Acropora patches in the reef lagoon. Density, colony size and living tissue cover of Acropora colonies were evaluated using the line-intercept transect technique, combining direct observations and video transects. The results showed that Acropora spp. was preferentially distributed in the southern regions; where cover and density were high. Based on these results and considering that Acropora spp. produces landscape heterogeneity, which in turn generates shelter for other species, including some of considerable economic importance, then at least the South East region should be considered as a key area for Acropora species conservation, and should be included in the Chinchorro Bank management plan.     

A novel red‐emitting phosphor,KAl1‐xPO4Cl:Eux3+ (0.1 ≤ x ≤ 1.0)

A series of phosphors KAl_1‐xPO₄Cl:Eu_x³⁺ (0.1 ≤ x ≤ 1.0) was synthesized using a facile combustion method using urea as a fuel and their structural, morphological and photoluminescence properties were investigated. It was found that the particle size was in the range of 1–2 µm with an irregular shape. The f–f transitions of Eu³⁺ in the host lattice were assigned and discussed. The excitation and emission spectra indicated that this phosphor can be efficiently excited by ultraviolet (395 nm), and exhibit reddish orange emission corresponding to the ⁵D₀→⁷F_J (J = 0, 1, 2) transitions of Eu³⁺. The impact of the Eu³⁺ concentration on the relative emission intensity was investigated, and the best doping concentration is 0.5. The present study suggests that the KAl_0.5PO₄Cl: Eu_0.5³⁺ phosphor is a strong candidate as a red component for phosphor‐ converted white light‐emitting diodes (LEDs). Copyright © 2015 John Wiley & Sons, Ltd.     

Luminescent properties of MAl(SO4)2Br:Eu3+ (M = Sr or Mg) red phosphors for near‐UV light‐emitting diodes

Eu³⁺‐activated MAl(SO₄)₂Br phosphors (where M = Mg or Sr) are successfully prepared using a wet chemical reaction technique. The samples are characterized by X‐ray diffraction (XRD) and photoluminescence (PL) spectroscopies. The XRD pattern revealed that both the samples are microcrystalline in nature. PL of Eu³⁺‐doped SrAl(SO₄)₂Br and MgAl(SO₄)₂Br phosphors exhibited characteristic red emission coming from the ⁵D₀ → ⁷F₂ (616 nm) electron transition, when excited by 396 nm wavelength of light. The maximum intensity of luminescence was observed at a concentration of 1 mol% Eu³⁺. The intensity of the electric dipole transition at 616 nm is greater than that of the magnetic dipole transition at 594 nm. The results showed that MAl(SO₄)₂Br:Eu³⁺, (M = Mg, Sr) phosphors have potential application in near‐UV light‐emitting diodes as efficient red‐emitting phosphor. Copyright © 2014 John Wiley & Sons, Ltd.