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The advent of molecular systematics has revolutionized our knowledge of biodiversity, revealing undiscovered cryptic lineages across the tree of life. Correspondingly, an increasing number of nudibranch species complexes have been found and described through integrative taxonomic approaches. Pteraeolidia ‘semperi’ (Nudibranchia: Cladobranchia: Aeolidioidea) presently represents a species complex, possessing ambiguous systematics and an underestimated diversity. Sequencing and phylogenetic reconstructions based on the cytochrome c oxidase subunit I marker from 48 samples of P. ‘semperi’ collected from Singapore's southern waters, as well as morphological analyses including scanning electron microscopy of the radula, suggest that P. ‘semperi’ comprises several distinct cryptic lineages. We further characterized the Symbiodiniaceae communities of P. ‘semperi’ from Singapore using metabarcoding of the internal transcribed spacer 2 gene. Pteraeolidia ‘semperi’ from Singapore was found to predominantly host Cladocopium and Durusdinium symbionts, and was significantly structured by biogeography. This study elucidates the present taxonomic diversity of P. ‘semperi’ in Singapore and contributes to the growing body of work on the diversity of algal symbionts associated with this enigmatic taxon.

Seagrass meadows are critical marine ecosystems. They are significant carbon sinks and play numerous important roles in coastal areas. They help to prevent shoreline erosion and serve as nursery grounds for many marine species. Like their terrestrial counterparts, seagrasses form symbiotic relationships with diverse communities of bacteria that help to promote and maintain host fitness. In this study, we sampled the seagrass Halophila ovalis throughout Singapore and Peninsular Malaysia to characterise the associated bacterial communities and distributions in this acknowledged seagrass biodiversity hotspot. Three different parts of the seagrass (leaves, roots and rhizomes) were collected, and a sediment sample was collected in close proximity to each host. We used high-throughput 16S rRNA amplicon sequencing to examine the bacterial communities associated with each plant part and location. Our analyses indicated that bacterial assemblages associated with H. ovalis were distinct among locations, and different plant parts harboured divergent bacterial communities. We uncovered a significant distance-decay relationship, suggesting that dispersal limitations could explain the observed bacterial community structuring. We further identified bacterial indicator amplicon sequence variants (ASVs) that were associated with degraded or healthy seagrass meadows. The identification of indicator ASVs that are indicative of anthropogenically stressed seagrass, or a declining environment, could be used to implement proactive seagrass conservation and management schemes. This study addresses a current scientific gap within the characterisation of seagrass microbiomes, specifically of those from Southeast Asia, a region of acute seagrass losses, and provides a solid foundation for future seagrass research in the region.

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.

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and without microbial cycling, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse of all the planets. They have vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and contain significant stocks of sequestered carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome are scarce, especially in the Southeast Asian biodiversity hotspot. Here we examine the microbiome ofAvicenia albaandSonneratia albaand identify a core microbiome of 81 taxa, a further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, andErythrobacter) were found to be differentially abundant suggesting key roles in this microbiome, with the identified dimethylsulfoniopropionate (DMSP) metabolisers having important functions in these habitats. The majority of those identified are involved in nutrient cycling or involved in the production of compounds that promote host survival. Increasingly, blue carbon and nature-based solutions to climate change are heralded as viable mitigation steps to limit climate change, however, this is done with little to no consideration of the microbial communities that cycle sequestered carbon in these environments. Here, we examine the microbial communities present in sediment samples taken in close proximity to each tree, sediment samples represent a major sink of atmospheric carbon and understanding how the associated communities will change as climate change advances will become an increasingly important part of carbon stock assessments. Knowing what microbes are presently there is an important first step in this process.

BackgroundSharks and rays are some of the most threatened marine taxa due to the high levels of bycatch and significant demand for meat and fin-related products in many Asian communities. At least 25% of shark and ray species are considered to be threatened with extinction. In particular, the density of reef sharks in the Pacific has declined to 3–10% of pre-human levels. Elasmobranchs are thought to be sparse in highly urbanised and turbid environments. Low visibility coupled with the highly elusive behaviour of sharks and rays pose a challenge to diversity estimation and biomonitoring efforts as sightings are limited to chance encounters or from carcasses ensnared in nets. Here we utilised an eDNA metabarcoding approach to enhance the precision of elasmobranch diversity estimates in urbanised marine environments.ResultsWe applied eDNA metabarcoding on seawater samples to detect elasmobranch species in the hyper-urbanised waters off Singapore. Two genes—vertebrate 12S and elasmobranch COI—were targeted and amplicons subjected to Illumina high-throughput sequencing. With a total of 84 water samples collected from nine localities, we found 47 shark and ray molecular operational taxonomic units, of which 16 had species-level identities. When data were compared against historical collections and contemporary sightings, eDNA detected 14 locally known species as well as two potential new records.ConclusionsLocal elasmobranch richness uncovered by eDNA is greater than the seven species sighted over the last two decades, thereby reducing phantom diversity. Our findings demonstrate that eDNA metabarcoding is effective in detecting shark and ray species despite the challenges posed by the physical environment, granting a more consistent approach to monitor these highly elusive and threatened species.

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.

Genetic population patterns in coral reefs are important for understanding biodiversity and forecasting recovery following disturbance. Studying gene flow between small and disrupted marine ecosystems, such as the reefs along the Singapore Strait, is especially crucial due to their fragile nature. Here we sampled the ubiquitous coral species complex Pachyseris speciosa from seven sites in Singapore and applied genotyping-by-sequencing (nextRAD) for a fine-scale population genomic assessment. Our results confirm the existence of two clearly distinct, possibly cryptic, lineages that occur sympatrically at each of the seven sampling sites and are related to the “blue” and “green” lineages found in other parts of the Indo-Pacific. The closely related lineages show contrasting patterns characterised by panmixia and substantial (but unexplained) substructuring, respectively. Analysis of barriers and corridors to gene flow reveals limited connectivity between the two largest clusters of reefs at the eastern and western sectors of Singapore’s southern coastal waters. Our results extend the geographic range of the two recently uncovered P. speciosa species, further confirming their status as distinct and widespread species. More broadly, our findings highlight how conservation and management strategies may maximise connectivity among Singapore’s urbanised reef ecosystems.

Despite their recognized importance in terrestrial and aquatic ecosystems, marine fungi, especially those associated with host organisms, remain poorly studied. Corals contain diverse communities of microbes that play important roles in adapting to disturbance and promoting host health, but studies on coral-associated fungal communities are conspicuous by their absence. Here, we comprehensively characterized the fungal communities and diversity associated with 97 unrelated coral colonies of Pocillopora acuta from nine islands in Singapore. We depleted coral DNA prior to PCR amplification of the fungal barcoding region (ITS1) to minimize issues of preferential host DNA amplification. This approach produced over a hundred times greater proportion of reads that were of fungal origin (75%) than previous studies, allowing us to more precisely characterize the associated fungal communities. We found no spatial structuring of fungal communities based upon sampling location, and provide evidence that suggests coral-associated fungi are more than just pathogens within their hosts. Many have been putatively identified as saprotrophs that are likely involved in making nutrients available for their host, and others may be possible symbiotrophs. Characterization of host-associated fungal communities provides valuable understanding—including information on the coral holobiont and how it functions—on a frequently overlooked, yet important microbial group.

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.

Background Experimental and clinical evidence support the role of macrophage Toll-like receptor signaling in maternal anti-SSA/Ro–mediated congenital heart block (CHB). Objectives Hydroxychloroquine (HCQ), an orally administered Toll-like receptor antagonist widely used in lupus including during pregnancy, was evaluated for efficacy in reducing the historical 18% recurrence rate of CHB. Methods This multicenter, open-label, single-arm, 2-stage clinical trial was designed using Simon’s optimal approach. Anti-SSA/Ro–positive mothers with a previous pregnancy complicated by CHB were recruited (n = 19 Stage 1; n = 35 Stage 2). Patients received 400 mg daily of HCQ prior to completion of gestational week 10, which was maintained through pregnancy. The primary outcome was 2° or 3° CHB any time during pregnancy, and secondary outcomes included isolated endocardial fibroelastosis, 1° CHB at birth and skin rash. Results By intention-to-treat (ITT) analysis, 4 of 54 evaluable pregnancies resulted in a primary outcome (7.4%; 90% confidence interval: 3.4% to 15.9%). Because 9 mothers took potentially confounding medications (fluorinated glucocorticoids and/or intravenous immunoglobulin) after enrollment but prior to a primary outcome, to evaluate HCQ alone, 9 additional mothers were recruited and followed the identical protocol. In the per-protocol analysis restricted to pregnancies exposed to HCQ alone, 4 of 54 (7.4%) fetuses developed a primary outcome as in the ITT. Secondary outcomes included mild endocardial fibroelastosis (n = 1) and cutaneous neonatal lupus (n = 4). Conclusions These prospective data support that HCQ significantly reduces the recurrence of CHB below the historical rate by >50%, suggesting that this drug should be prescribed for secondary prevention of fetal cardiac disease in anti-SSA/Ro-exposed pregnancies. (Preventive Approach to Congenital Heart Block With Hydroxychloroquine [PATCH]; NCT01379573 )

Autoimmune-mediated congenital heart block (CHB) is a severe manifestation of neonatal lupus in which conduction tissues of the fetal heart are damaged. This occurs due to passive transference of maternal anti-SSA/Ro and anti-SSB/La autoantibodies and subsequent inflammation and fibrosis of the atrioventricular (AV) node. Notably, the disease manifests after the fetal heart has structurally developed, ruling out other anatomical abnormalities that could otherwise contribute to the block of conduction. Complete AV block is irreversible and the most common manifestation of CHB, although other cardiac complications such as endocardial fibroelastosis (EFE), dilated cardiomyopathy, and valvular insufficiency have been observed. In this review, we detail the classification, prevalence, pathogenesis, and clinical management recommendations for autoimmune CHB.

Many corals depend upon the highly specialised and intricate relationship they form with Symbiodiniaceae algal symbionts. Porites lutea is a massive reef-building coral found throughout Southeast Asia that hosts these endosymbionts obligately. Yet despite the prevalence and importance of P. lutea as one of the most dominant corals here, its associated Symbiodiniaceae communities have not been precisely characterised. In this study, we used high-throughput DNA amplicon sequencing of the nuclear internal transcribed spacer 2 (ITS2) to characterise the diversity, community structure and biogeographic distribution of Symbiodiniaceae in P. lutea throughout Singapore and Peninsular Malaysia. Consistent with previous studies, we found that Cladocopium was the most dominant genus among all samples, and Cladocopium C15 was the most dominant type (or subclade) with 100% occurrence in all samples from every study site. Results also revealed numerous Symbiodiniaceae types associated with P. lutea that were previously undetected in Southeast Asia. Endosymbiont diversity and community variation are driven by a combination of site-specific mean monthly cloud cover and variance in monthly sea surface temperature. This study contributes baseline data toward understanding differences in Symbiodiniaceae assemblages hosted by P. lutea, shedding light on how they might be indicative of particular environmental conditions and coral responses.

Accurate identification and association of larval specimens with adults is a major challenge in insect taxonomy. Fortunately, it is now possible for nonexperts to sort collections of bulk samples with DNA barcodes rapidly and cost-effectively. We demonstrate this process using nanopore barcoding of 757 marine insects (Insecta: Gerromorpha), of which 81% were nymphs and many samples did not have co-occurring adult males for specific identification. We successfully associated 738 specimens (97%) to nine gerromorphan species, which would have been impossible to identify using morphological characters alone. This improved ability to incorporate information from all life-history stages has led to greater precision of species distributional ranges—knowledge that will be crucial for a more complete understanding of marine insects. We also highlighted two distinct, nonoverlapping Gerromorpha COI sequence databases on GenBank—a consequence of using two different primer sets to amplify different regions of COI. This issue inevitably hinders species identification with DNA-based methods, particularly for poorly represented groups such as marine insects. We bridged these databases by analyzing full-length COI sequences. We believe this will inspire future studies to incorporate DNA-based methods for more adult–larval association studies and for enhancing existing genetic resources, especially in understudied groups.

The atmosphere is the least understood biome on Earth despite its critical role as a microbial transport medium. The influence of surface cover on composition of airborne microbial communities above marine systems is unclear. Here we report evidence for a dynamic microbial presence at the ocean–atmosphere interface of a major marine ecosystem, the Great Barrier Reef, and identify that recent air mass trajectory over an oceanic or continental surface associated with observed shifts in airborne bacterial and fungal diversity. Relative abundance of shared taxa between air and coral microbiomes varied between 2.2 and 8.8% and included those identified as part of the core coral microbiome. We propose that this variable source of atmospheric inputs may in part contribute to the diverse and transient nature of the coral microbiome.

Marine environments abound with opportunities to discover new species of fungi even in relatively well-studied ecosystems such as coral reefs. Here, we investigated the fungal communities associated with the canopy forming macroalga Sargassum ilicifolium(Turner) C. Argardh (1820) in Singapore. We collected eight S. ilicifolium thalli from each of eight island locations and separated them into three structures—leaves, holdfast and vesicles. Amplicon sequencing of the fungal internal transcribed spacer 1 (ITS1) and subsequent analyses revealed weak but significant differences in fungal community composition from different structures. Fungal communities were also significantly different among sampling localities, even over relatively small spatial scales (≤ 12 km). Unsurprisingly, all structures from all localities were dominated by unclassified fungi. Our findings demonstrate the potential of marine environments to act as reservoirs of undocumented biodiversity that harbour many novel fungal taxa. These unclassified fungi highlight the need to look beyond terrestrial ecosystems in well-studied regions of the world, and to fully characterize fungal biodiversity in hotspots such as Southeast Asia for better understanding the roles they play in promoting and maintaining life on our planet.

The coral holobiont contains a diverse community of bacteria that have been widely acknowledged as a major contributor in the maintenance of host health and in promoting reef resilience under changing environments. However, little is known regarding the spatial distribution of these communities or the processes and mechanisms that are responsible for creating these patterns. Here we show that bacterial communities associated with the reef-building coral, Pocillopora acuta, from nine offshore islands in an urbanised coral reef ecosystem (Singapore) can diverge sharply and are significantly different among sampling locations. We suggest that small-scale environmental factors such as prevailing surface currents and wind direction, even over short distances (

Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.

In 1%–18% of pregnancies, fetal exposure to maternal anti-SSA/Ro and anti-SSB/La autoantibodies transported across the placenta via FcγRn can result in a spectrum of injury referred to as neonatal lupus. Disease in the offspring may be independent of the maternal health status as often the mother has no previous history of any autoimmune or rheumatic disorder. The classic manifestations include cardiac injury in utero and a cutaneous rash in the neonatal period though other organ systems may be affected as well. The antibodies associating with injury are reactive with an intracellular target, providing a rare opportunity to evaluate pathways leading to autoimmune-mediated tissue injury and to translate these findings to management. This chapter extensively covers the epidemiology, clinical spectrum, proposed pathogenesis, biomarkers, and guidelines for prevention and therapy, taking into account new advances from the bench and bedside, including the introduction of home monitoring.

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.

Thermal stress drives the bleaching of reef corals, during which the endosymbiotic relationship between Symbiodiniaceae microalgae and the host breaks down. The endosymbiont communities are known to shift in response to environmental disturbances, but how they respond within and between colonies during and following bleaching events remains unclear. In 2016, a major global-scale bleaching event hit countless tropical reefs. Here, we investigate the relative abundances of Cladocopium LaJeunesse &amp, H.J.Jeong, 2018 and Durusdinium LaJeunesse, 2018 within and among Pachyseris speciosa colonies in equatorial Singapore that are known to host both these Symbiodiniaceae clades. Bleached and unbleached tissues from bleaching colonies, as well as healthy colonies, during and following the bleaching event were sampled and analyzed for comparison. The nuclear ribosomal internal transcribed spacer (ITS) regions were separately amplified and quantified using a SYBR Green-based quantitative polymerase chain reaction (qPCR) method and Illumina high-throughput sequencing. We found Cladocopium to be highly abundant relative to Durusdinium. The relative abundance of Durusdinium, known to be thermally tolerant, was highest in post-bleaching healthy colonies, while bleached and unbleached tissues from bleaching colonies as well as tissue from healthy colonies during the event had depressed proportions of Durusdinium. Given the importance of Durusdinium for thermal tolerance and stress response, it is surprising that bleached tissue showed limited change over healthy tissue during the bleaching event. Moreover, colonies were invariably dominated by Cladocopium during bleaching, but a minority of colonies were Durusdinium-dominant during non-bleaching times. The detailed characterization of Symbiodiniaceae in specific colonies during stress and recovery will provide insights into this crucial symbiosis, with implications for their responses during major bleaching events.

The shark and ray (Elasmobranchii) trade is a commercially valuable industry that has negative consequences for wild populations. An estimated 100 million sharks are caught each year to supply the demand for cultural cuisines, traditions and practices, including shark fin soup and Traditional Chinese Medicine. Despite the establishment of frameworks and regulations by international trade and conservation bodies as well as national legislations, elasmobranch populations continue to decline. While their conservation becomes an ever more pressing concern, a major obstacle that hampers regulation is the mislabelling and/or misidentification of dried products or carcasses that have had fins removed. Here we use DNA barcoding to identify the species of origin for a variety of shark and ray products readily available to consumers in Singapore, a major importer of these goods. We amplified a fragment of the cytochrome c oxidase subunit I gene from shark fin, cartilage and meat, as well as ray gill plates and meat for DNA sequencing. Our analysis of 207 DNA barcodes yielded 28 positively identified elasmobranch species, eight of which are listed under Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, and 12 are listed as Endangered or Vulnerable by the International Union for the Conservation of Nature. This information will be useful to regulatory bodies in controlling trade and establishing new or revisiting previous conservation status listings.

The population genetics of two seagrasses,Syringodium isoetifoliumandThalassia hemprichiiwere assessed throughout the Indonesian Archipelago. We genotyped 257 blades ofS.isoetifoliumat 15 microsatellite loci collected from 14 sampling sites and 406 blades ofT. hemprichiiat 17 microsatellite loci from 16 sampling sites. Once clones were removed, 165 individuals ofS.isoetifoliumand 389 ofT. hemprichiiwere used in downstream analyses. Bayesian clustering methods revealed two genetically distinguishable clusters in each species, although the geographic boundaries of these clusters differed.Syringodium isoetifoliumhas a cluster that is located exclusively on the shallow Sunda Shelf and appears to follow the demarcation defined by Wallace’s line.Thalassia hemprichii, however, has a genetically distinguishable cluster located within the Banda Sea. The Banda Sea has unique physical oceanographic conditions, which may be driving the observed differentiation inT. hemprichii. We speculate that historical sea level changes exposing the Sunda Shelf, and the unique oceanographic conditions of the Banda Sea are contributing to the observed population differentiation. The observed genetic differentiation in both species is a possible starting point for speciation.