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Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls. However, the intertidal section of coastal armour is a challenging environment for corals, with conditions during periods of emersion being particularly stressful. Here, we scanned the entire genome of P. acuta corals to identify the regions harbouring single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) that separate intertidal colonies (n = 18) from those found in subtidal areas (n = 21). Findings revealed 74,391 high quality SNPs distributed across 386 regions of the P. acuta genome. While the majority of the detected SNPs were in non-coding regions, 12% were identified in exons (i.e. coding regions). Functional SNPs that were significantly associated with intertidal colonies were found in overrepresented genomic regions linked to cellular homeostasis, metabolism, and signalling processes, which may represent local environmental adaptation in the intertidal. Interestingly, regions that exhibited CNVs were also associated with metabolic and signalling processes, suggesting P. acuta corals living in the intertidal have a high capacity to perform biological functions critical for survival in extreme environments. [ABSTRACT FROM AUTHOR]

Waminoa spp. are acoel flatworms mainly found as ectosymbionts on scleractinian corals. Although Waminoa could potentially represent a threat to their hosts, not enough information is available yet regarding their ecology and effect on the coral. Here, the Waminoa sp.–coral association was analyzed in Singapore reefs to determine the prevalence, host range, and preference, as well as the flatworm abundance on the coral surface. Moreover, the impact of Waminoa sp. on the expression of putative immune- and stress-response genes (C-type lectin, C3, Hsp70 and Actin) was examined in the coral Lobophyllia radians. The association prevalence was high (10.4%), especially in sites with lower sedimentation and turbidity. Waminoa sp. showed a wide host range, being found on 17 coral genera, many of which are new association records. However, only few coral genera, mostly characterized by massive or laminar morphologies appeared to be preferred hosts. Waminoa sp. individuals displayed variable patterns of coral surface coverage and an unequal distribution among different host taxa, possibly related to the different coral growth forms. A down-regulation of the expression of all the analyzed genes was recorded in L. radians portions colonized by Waminoa individuals compared to those without. This indicated that Waminoa sp. could affect components of the immune system and the cellular homeostasis of the coral, also inhibiting its growth. Therefore, Waminoa sp. could represent a potential further threat for coral communities already subjected to multiple stressors. [ABSTRACT FROM AUTHOR]

Abstract: The Coral Triangle (CT) region of the Indo‐Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time‐calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model‐based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long‐standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas. [ABSTRACT FROM AUTHOR]

Hexahydroxy-stannates (MSn(OH) 6 ) are promising candidates for photocatalytic degradation of highly stable aromatic compounds. A series of MSn(OH) 6 (MHS, M = Co, Cu, Fe, Mg, Mn, Zn) was synthesized by a hydrothermal method in this work. The effects of the hydrothermal temperature, time and the solution pH on the formation of MHS were investigated. The structures, yields, optical properties, and morphologies of the products were then studied. Photocatalytic degradation of gaseous benzene (C 6 H 6 ) on the prepared MHS was investigated and compared with P25 (TiO 2 ). The results indicate the optimal preparation condition of MHS is performing the hydrothermal treatment at a mild temperature (90–120 °C) in a weak base solution (pH 10–11). Only MgHS and ZnHS exhibit a significant and stable activity for the destruction of C 6 H 6 and the efficiencies are substantially higher than that of P25. The hydroxyl structure accounts for their high performance, which facilitates the formation of the active radicals ( OH and O 2 − ) and suppresses the deposition of the stable byproducts. Due to the restriction of the band structures, the degradation of C 6 H 6 cannot be achieved on the colored samples (M = Co, Cu, Fe, and Mn). Based on the radicals analyses results, the degradation route of C 6 H 6 on and the formation route of the stable intermediates on the samples were finally proposed. [ABSTRACT FROM AUTHOR]

Highlights: [•] ZHS surface microstructure and photocatalytic performance are sensitive to preparation method. [•] A harsh preparation condition leads to OH-unsaturated Zn and Sn atoms. [•] ZHS prepared by PVP-assisted hydrothermal method exhibits the highest activity. [ABSTRACT FROM AUTHOR]

Background: Molecular phylogenetic studies on scleractinian corals have shown that most taxa are not reflective of their evolutionary histories. Based principally on gross morphology, traditional taxonomy suffers from the lack of well-defined and homologous characters that can sufficiently describe scleractinian diversity. One of the most challenging clades recovered by recent analyses is 'Bigmessidae', an informal grouping that comprises four conventional coral families, Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae, interspersed among one another with no apparent systematic pattern. There is an urgent need for taxonomic revisions in this clade, but it is vital to first establish phylogenetic relationships within the group. In this study, we reconstruct the evolutionary history of 'Bigmessidae' based on five DNA sequence markers gathered from 76 of the 132 currently recognized species collected from five reef regions in the central Indo-Pacific and the Atlantic. Results: We present a robust molecular phylogeny of 'Bigmessidae' based on the combined five-gene data, achieving a higher degree of resolution compared to previous analyses. Two Pacific species presumed to be in 'Bigmessidae' are more closely related to outgroup clades, suggesting that other unsampled taxa have unforeseen affinities. As expected, nested within 'Bigmessidae' are four conventional families as listed above, and relationships among them generally corroborate previous molecular analyses. Our more resolved phylogeny supports a close association of Hydnophora (Merulinidae) with Favites + Montastraea (Faviidae), rather than with the rest of Merulinidae, i.e., Merulina and Scapophyllia. Montastraea annularis, the only Atlantic 'Bigmessidae' is sister to Cyphastrea, a grouping that can be reconciled by their septothecal walls, a microstructural feature of the skeleton determined by recent morphological work. Characters at the subcorallite scale appear to be appropriate synapomorphies for other subclades, which cannot be explained using macromorphology. Indeed, wide geographic sampling here has revealed more instances of possible cryptic taxa confused by evolutionary convergence of gross coral morphology. Conclusions: Numerous examples of cryptic taxa determined in this study support the assertion that diversity estimates of scleractinian corals are erroneous. Fortunately, the recovery of most 'Bigmessidae' genera with only minor degrees of paraphyly offers some hope for impending taxonomic amendments. Subclades are well defined and supported by subcorallite morphological features, providing a robust framework for further systematic work. [ABSTRACT FROM AUTHOR]

The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the “barcoding gap” does not improve identification success. [ABSTRACT FROM AUTHOR]

Aim: Giant clams are iconic bivalves known to serve numerous ecological roles contributing to the functioning of coral reef ecosystems. In the next decade, giant clams will continue to face critical anthropogenic pressures from over‐exploitation for their meat and shells, the aquarium trade and global warming that threaten the persistence of their species. Here, we assess the relationships between different biodiversity components to inform conservation prioritization and management. Location: Indo‐Pacific marine realm. Methods: We quantified taxonomic, functional and phylogenetic diversity measures throughout 25 marine provinces and assessed their relationships for all 12 giant clam species in the subfamily Tridacninae. These biodiversity measures were used to identify potentially threatened species that contribute disproportionately to trait and evolutionary diversity and to highlight areas for global conservation prioritization of giant clam species. Results: Analyses show positive correlations among species richness (SR), functional diversity (FD) and phylogenetic diversity (PD), with the strongest relationship between FD and PD. However, spatial patterns of higher‐than‐expected FD and PD are incongruent with SR patterns, indicating that SR omits information associated with functional and phylogenetic diversity. Among the giant clam species, Tridacna gigas and Hippopus spp. have the greatest functional and evolutionary diversity contributions within assemblies, respectively. Spatial analyses reveal that the Bay of Bengal, Andaman and numerous parts of the eastern Indo‐Pacific potentially hold higher‐than‐expected FD and PD levels relative to their SR and thus warrant more attention with respect to conserving the diversity of giant clams. Conclusions: Our findings underscore the importance of integrating functional trait contributions and evolutionary diversity into conservation planning to better differentiate giant clam assemblages, as it remains challenging to implement dedicated conservation given the limited resources. This study provides comprehensive biodiversity information for managers to initiate measures that holistically capture species' ecological and evolutionary standings across global reef ecosystems. [ABSTRACT FROM AUTHOR]

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate. [ABSTRACT FROM AUTHOR]

Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems. [ABSTRACT FROM AUTHOR]

A new zooxanthellate reef-dwelling scleractinian coral species, Cyphastrea salae sp. n. (Scleractinia, Merulinidae), is described from Lord Howe Island Australia. The new species can be distinguished morphologically from the only other congeneric species on Lord Howe Island, C. microphthalma, by the number of primary septa (12 vs. 10) and the much taller corallites (mean ± SE: 1.0 ± 0.07 mm v 0.4 ± 0.04 mm). The relationship of C. salae to four of the other eleven currently accepted species in the genus was explored through analyses of nuclear (28S rDNA) and mitochondrial (noncoding intergenic region) gene sequences. Cyphastrea salae sp. n. forms a strongly supported clade that is distinct from a clade containing three species found commonly in Australia, C. chalcidicum, C. serailia, and C. microphthalma. One specimen was also found in the Solitary Islands, another high latitude location in south-eastern Australia. The discovery of a new species in the genus Cyphastrea on high latitude reefs in south-eastern Australia suggests that other new species might be found among more diverse genera represented here and that the scleractinian fauna of these isolated locations is more distinct than previously recognised. [ABSTRACT FROM AUTHOR]

Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare. [ABSTRACT FROM AUTHOR]

Aim: The ecosystem functions and services of coral reefs are critical for coastal communities worldwide. Due to conservation resource limitation, species need to be prioritized to protect desirable properties of biodiversity, such as functional diversity (FD), which has been associated with greater ecosystem functioning but is difficult to quantify directly. Selecting species to maximize phylogenetic diversity (PD) has been shown to indirectly capture FD in certain other taxa but not corals. Here, we test this hypothesis, the "phylogenetic gambit", on corals within global marine protected areas (MPAs). Location: Global coral reefs. Methods: Based on the global distributions of reef corals, a complete species‐level phylogeny and trait data, we compared the FD of coral assemblages within MPAs when selected to maximize PD versus FD for assemblages selected randomly. The relationships between PD and FD were also tested as predictors of surrogacy. We then used coral FD and PD to perform spatial prioritization of reefs for protection and assessed the congruence between the two approaches. Results: Selecting assemblages to maximize PD captured significantly more FD than a random subset of species for 83.1% of all selection scenarios across MPAs and would protect on average 18.7% more FD than random selection. Spatial prioritization analyses showed some mismatches between PD‐ and FD‐optimized planning units, particularly in the Tropical Western Atlantic, but the high degree of overlap between the optimizations for other reef regions lends further credence to the PD‐maximizing strategy in conserving coral FD. Main Conclusions: A PD‐maximizing strategy generally protects greater FD of coral assemblages relative to random selection of species, suggesting that the "phylogenetic gambit" is valid for reef corals. There are risks, however, and the mismatches between PD‐maximized and FD‐maximized MPA networks highlight specific shortcomings of the PD‐maximization approach. Nevertheless, in data‐deficient circumstances, maximizing PD may provide a viable alternative. [ABSTRACT FROM AUTHOR]

• Understanding spatial and temporal trends of diversity is crucial for conservation. • This study analyses long-term data from 1986 to 2020 on Singapore reefs. • Taxonomic and phylogenetic diversity increased but functional diversity declined. • Reefs shifted towards dominance of stress-tolerant traits such as slow growth. • Trait-based approaches at finer taxonomic resolution will enhance reef monitoring. Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution. [ABSTRACT FROM AUTHOR]

Summary: Distributed across both the tropical Atlantic and Pacific oceans, the seagrass Halophilia ovalis stabilizes coastal sediment, thereby preventing shoreline erosion and is also an important food source for megaherbivores such as dugongs. However, seagrass meadows globally are under severe duress due to both climate change and anthropogenic activities. We characterized the mycobiome of Halophilia ovalis at seven sites in the Malay Peninsula using ITS1 rDNA amplicon sequences and investigated differences in fungal community structure. We found that geographic location was a significant factor shaping fungal communities and that marine sediment harboured significantly higher diversity when compared to H. ovalis leaves, roots and rhizomes. Taken together, it is likely that locality rather than specific plant structure determines fungal community structure in H. ovalis. Because the plant mycobiome is known to exert a strong effect on plant health, to maximize the success of future seagrass transplantation and restoration work we propose that these efforts consider the importance of seagrass mycobiomes at all stages. [ABSTRACT FROM AUTHOR]

Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore's urbanized equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef‐building corals with distinct life histories. For Porites sp., a broadcast‐spawning coral, we found cryptic lineages that were differentially distributed at inshore and central‐offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60–80% of colonies in each population were nonmigrants, underscoring self‐recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore's coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in South‐East Asia. [ABSTRACT FROM AUTHOR]

Species boundaries delineating tropical sea anemones (Cnidaria, Actiniaria) of the zooxanthellate genus, Heteranthus Klunzinger, 1877, are unclear. There are currently two valid Heteranthus species: type species Heteranthus verruculatus Klunzinger, 1877, first reported from Koseir, Egypt, and H. insignis Carlgren, 1943, from Poulo Condore, Vietnam. In describing the latter from a single, poorly preserved specimen, zoologist Oskar Carlgren expressed apprehension with traits he had used to establish this species. Carlgren's doubts persisted later in writing when he found a similar-looking sea anemone from the Great Barrier Reef. Crucial details to positively identify either species have since remained limited. Here, we re-diagnosed Heteranthus and re-described its type species based on observations of specimens we have obtained from Singapore and Pulau Ambon (Indonesia), and of museum material collected elsewhere across the Indo-West Pacific region (n > 180). Supported by molecular phylogenetic evidence, the family Heteranthidae Carlgren, 1900 was reinstated and re-diagnosed. Heteranthus verruculatus is encountered in the lower intertidal region amongst seagrass, in rocky crevices, or coral rubble. It occurs as solitary individuals or in clonal clusters, well-camouflaged against the substratum. Individuals were observed to frequently propagate by longitudinal fission, resulting in a varied appearance. Type material of H. verruculatus and H. insignis were re-examined and as we found no differences between them, the two were synonymised. We inferred that Carlgren probably misinterpreted cnidae and histological data in defining H. insignis as a distinct species. This revision clarifies the taxonomy and geographic range of H. verruculatus, an Indo-West Pacific species that is found from the Red Sea to subtropical Australia and Hawaii. [ABSTRACT FROM AUTHOR]

Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme. [ABSTRACT FROM AUTHOR]

Abstract: Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (FST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat. [ABSTRACT FROM AUTHOR]

• Bacterial communities are temporally dynamic whereas Symbiodiniaceae are stable in an equatorial reef system. • No monsoonal or environmental effect on any directional shifts in bacterial communities. • Partnerships between bacteria and Symbiodiniaceae members are associated with biogeochemical and physiological processes. • Long-term studies shed insight into holobiont community dynamics and are critical in guiding restoration efforts. Coral-associated bacteria and Symbiodiniaceae are critical for maintaining the health of their coral hosts. Factors that are known to affect the coral microbiome include biogeography, seasonality, and environmental change, but longitudinal studies are sorely lacking. Many temporal studies rarely extend beyond a year, limiting the conclusions that can be drawn. In this study, we characterised both the bacterial and Symbiodiniaceae communities in three species of corals— Merulina ampliata , Pachyseris speciosa , and Porites lutea —found in an equatorial reef over a two-year period. Furthermore, we investigated the effect of monsoon seasons on the pattern of bacterial and Symbiodiniaceae communities using metabarcoding methods. We found significant differences in bacterial communities through time and space, but no consistent patterns of diversity between seasons and environmental conditions (temperature and rainfall) were observed. Conversely, Symbiodiniaceae communities did not differ over time and space. Taken together, our results suggest that bacterial communities, even within a stable climate regime, were highly dynamic through time, but were not affected by monsoonal variations. Finally, network analyses of bacteria and Symbiodiniaceae revealed multiple potential biogeochemical processes that worked in tandem between the members of the coral holobiont to support holobiont functioning. Longitudinal studies on host-associated microbial diversity are critical for drawing relevant conclusions about the long-term effects of environmental change on the coral holobiont, and for directing conservation efforts. [ABSTRACT FROM AUTHOR]

Sea anemones are sedentary marine animals that tend to disperse via planktonic larvae and are predicted to have high population connectivity in undisturbed habitats. We test whether two sea anemone species living in two different tidal zones of a highly disturbed marine environment can maintain high genetic connectivity. More than 1000 loci with single-nucleotide polymorphisms (SNPs) were obtained with double-digest RADseq for 81 Stichodactyla haddoni and 99 Entacmaea quadricolor individuals to test for population genetic structure. We find evidence that both species predominantly propagate via sexual reproduction, and asexual reproduction is limited. We observe panmixia that indicates the absence of effective dispersal barriers for these species living in a highly anthropogenically disturbed environment. This is positive news for both species that are also found in the aquarium trade. More fundamentally, our results suggest that inhabiting different parts of a shallow reef may not affect a species' population connectivity nor favour asexual reproduction. [ABSTRACT FROM AUTHOR]

Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia. [ABSTRACT FROM AUTHOR]

Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. [ABSTRACT FROM AUTHOR]

Corals harbour diverse microbial communities that can change in composition as the host grows in age and size. Larger and older colonies have been shown to host a higher diversity of microbial taxa and this has been suggested to be a consequence of their more numerous, complex and varied micro-niches available. However, the effects of host age on community structure and diversity of microbial associates remain equivocal in the few studies performed to date. To test this relationship more robustly, we use established techniques to accurately determine coral host age by quantifying annual skeletal banding patterns, and utilise high-throughput sequencing to comprehensively characterise the microbiome of the common reef-building coral, Porites lutea. Our results indicate no clear link between coral age and microbial diversity or richness. Different sites display distinct age-dependent diversity patterns, with more anthropogenically impacted reefs appearing to show a winnowing of microbial diversity with host age, possibly a consequence of corals adapting to degraded environments. Less impacted sites do not show a signature of winnowing, and we observe increases in microbial richness and diversity as the host ages. Furthermore, we demonstrate that corals of a similar age from the same reef can show very different microbial richness and diversity. [ABSTRACT FROM AUTHOR]

Background: Recent taxonomic revisions of zooxanthellate scleractinian coral taxa have inevitably resulted in confusion regarding the geographic ranges of even the most well-studied species. For example, the recorded distribution ranges of Stylophora pistillata and Pocillopora damicornis, two of the most intensely researched experimental subjects, have been restricted dramatically due to confounding cryptic species. Micromussa is an Indo-Pacific genus that has been revised recently. The revision incorporated five new members and led to substantial range restriction of its type species and only initial member M. amakusensis to Japan and the Coral Triangle. Here, we report the presence of Micromussa amakusensis in Singapore using phylogenetic methods. Results: A total of seven M. amakusensis colonies were recorded via SCUBA surveys at four coral reef sites south of mainland Singapore, including two artificial seawall sites. Colonies were found encrusting on dead coral skeletons or bare rocky substrate between 2 and 5 m in depth. Morphological examination and phylogenetic analyses support the identity of these colonies as M. amakusensis, but the phylogeny reconstruction also shows that they form relatively distinct branches with unexpected lineage diversity. Conclusions: Our results and verified geographic records of M. amakusensis illustrate that, outside the type locality in Japan, the species can also be found widely in the South China Sea. Moreover, our discovery provides a new genus and species record in Singapore and represents the southern-most occurrence of the species in the Indo-Pacific. Despite the extensive survey efforts in Singapore over the last three decades, taxonomic studies integrating morphological and molecular methods remain instrumental in quantifying the actual coral species diversity. [ABSTRACT FROM AUTHOR]

Summary Mutually beneficial interactions between species (mutualisms) shaped the evolution of eukaryotes and remain critical to the survival of species globally [ 1, 2 ]. Theory predicts that hosts should pass mutualist symbionts to their offspring (vertical transmission) [ 3–8 ]. However, offspring acquire symbionts from the environment in a surprising number of species (horizontal acquisition) [ 9–12 ]. A classic example of this paradox is the reef-building corals, in which 71% of species horizontally acquire algal endosymbionts [ 9 ]. An untested hypothesis explaining this paradox suggests that horizontal acquisition allows offspring to avoid symbiont-induced harm early in life. We reconstructed the evolution of symbiont transmission across 252 coral species and detected evolutionary transitions consistent with costs of vertical transmission among broadcast spawners, whose eggs tend to be positively buoyant and aggregate at the sea surface. Broadcasters with vertical transmission produce eggs with traits that favor reduced buoyancy (less wax ester lipid) and rapid development to the swimming stage (small egg size), both of which decrease the amount of time offspring spend at the sea surface. Wax ester provisioning decreased after vertically transmitting species evolved brooding from broadcasting, indicating that reduced buoyancy evolves only when offspring bear symbionts. We conclude that horizontal acquisition protects offspring from damage caused by high light and temperatures near the sea surface while providing benefits from enhanced fertilization and outcrossing. These findings help explain why modes of symbiont transmission and reproduction are strongly associated in corals and highlight benefits of delaying mutualist partnerships, offering an additional hypothesis for the pervasiveness of this theoretically paradoxical strategy. [ABSTRACT FROM AUTHOR]