Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats

First record of a neonate bluntnose sixgill shark (Hexanchus griseus) from Baja California Sur, Mexico

The bluntnose sixgill shark (Hexanchus griseus) is a wide-ranged deep-water shark species found off continental and insular shelves. Despite its global distribution, little is known about the reproductive ecology of the species, particularly with regard to the location and timing of important phenological events such as mating and pupping. In this study, we report the landing of a neonate H. griseus individual from an artisanal fishing camp in Baja California Sur, Mexico. This represents only the ninth confirmed record of the species from the Mexican Pacific and the first to report a neonate specimen in Mexican waters. We discuss this specimen in the context of the environmental conditions in which it was found, ultimately suggesting that these shallow coastal waters may be an important pupping ground for H. griseus in the region. Furthermore, the specimen was found during the winter months (whereas all previous reports have suggested H. griseus pups during the summer), implying regional variation in reproductive periodicity, or the presence of multiple reproductive events per year. This study provides novel insight into the reproductive biology of H. griseus and the ecological characteristics of the species in the Northern Mexican Pacific.

Species-specific eDNA assay development for enhanced box jellyfish risk management in coastal environments

Human interaction with marine creatures holds both positive and negative dimensions. Coastal communities benefit from marine environments, relying on them for sustenance and livelihoods. Fishing activities support economies, and marine biodiversity contributes to overall ecosystem health. However, challenges like overfishing, habitat destruction, and pollution pose threats to both marine life and human communities. Recently, there has been widespread concern regarding the potential increase in jellyfish populations across global marine ecosystems, attributed mainly to environmental factors such as climate drivers and anthropogenic forces, or their complex interactions. Encounters with hazardous marine species, such as box jellyfish, exemplify the dangers associated with coastal activities. Unintended interactions may lead to stings, injuries, and even fatalities, necessitating proactive measures and advanced technologies. This study addresses the inadequacies of existing measures in preventing box jellyfish incidents by introducing environmental DNA (eDNA) assays for detecting the deadly Chiropsoides buitendijki and focuses on developing qPCR and dPCR-based eDNA assays. Emphasising prevention over treatment, the study establishes a proactive system to assess C. buitendijki distribution across 63 tourist beaches in the Gulf of Thailand. Comparative analysis highlights the superior performance of dPCR over qPCR and traditional surveys. The dPCR experiment yielded positive results for all eDNA samples collected at sites where C. buitendijki had previously been identified. Remarkably, the eDNA testing also detected positive results in 16 additional sample locations where no physical specimens were collected, despite reported jellyfish stings at some of these sites. These findings underscore the precision and efficacy of the proposed eDNA detection technology in the early detection and assessment of box jellyfish distribution. This advancement therefore not only aids ecological research but also serves as a valuable tool for safeguarding public health, providing an early warning system for potential jellyfish encounters. Balancing positive human-marine interactions with effective risk mitigation strategies is crucial for sustainable coexistence, the preservation of marine ecosystems, and human well-being.

Can denticle morphology help identify southeastern Australian elasmobranchs?

Elasmobranchs are covered in scale-like structures called dermal denticles, comprising dentine and enameloid. These structures vary across the body of an individual and between species, and are frequently shed and preserved in marine sediments. With a good understanding of denticle morphology, current and historical elasmobranch diversity and abundance might be assessed from sediment samples. Here, replicate samples of denticles from the bodies of several known (deceased) shark species were collected and characterized for morphology before being assigned morphotypes. These data were used to expand the established literature describing denticles and to investigate intra- and interspecific variability, with the aim of increasing the viability of using sediment samples to assess elasmobranch diversity and abundance. Denticle morphology was influenced more by life-history traits than by species, where demersal species were largely characterized by generalized function and defense denticles, whereas pelagic and benthopelagic species were characterized by drag-reduction denticles. Almost all species possessed abrasion strength or defense denticles on the snout, precluding their utility for separating species. In a separate manipulative experiment, samples of denticles were collected from sediments in two aquaria with known elasmobranchs to determine their utility for reliably separating species. Visual examination of denticles, morphometric measurements, scaled photographs, and reference collections allowed for some precise identification, but not always to the species level. Ongoing work to develop denticle reference collections could help to identify past and present families and, in some cases, species.

DNA barcoding continues to identify endangered species of shark sold as food in a globally significant shark fin trade hub

Shark fins are a delicacy consumed throughout Southeast Asia. The life history characteristics of sharks and the challenges associated with regulating fisheries and the fin trade make sharks particularly susceptible to overfishing. Here, we used DNA barcoding techniques to investigate the composition of the shark fin trade in Singapore, a globally significant trade hub. We collected 505 shark fin samples from 25 different local seafood and Traditional Chinese Medicine shops. From this, we identified 27 species of shark, three species are listed as Critically Endangered, four as Endangered and ten as Vulnerable by the International Union for Conservation of Nature (IUCN). Six species are listed on CITES Appendix II, meaning that trade must be controlled in order to avoid utilization incompatible with their survival. All dried fins collected in this study were sold under the generic term "shark fin"; this vague labelling prevents accurate monitoring of the species involved in the trade, the effective implementation of policy and conservation strategy, and could unwittingly expose consumers to unsafe concentrations of toxic metals. The top five most frequently encountered species in this study are Rhizoprionodon acutus, Carcharhinus falciformis, Galeorhinus galeus, Sphyrna lewini and Sphyrna zygaena. Accurate labelling that indicates the species of shark that a fin came from, along with details of where it was caught, allows consumers to make an informed choice on the products they are consuming. Doing this could facilitate the avoidance of species that are endangered, and similarly the consumer can choose not to purchase species that are documented to contain elevated concentrations of toxic metals.

Multispecies environmental DNA metabarcoding sheds light on annual coral spawning events

Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral-ITS2 and vertebrate-12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five-fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night- and day-time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events.

Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area

Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

What Is in Your Shark Fin Soup? Probably an Endangered Shark Species and a Bit of Mercury

Simple Summary

Shark fin soup is consumed by many Asian communities throughout the world and is one of the main drivers of the demand for shark fin. The demand for shark products has seen shark populations decline by as much as 70%. The fins found in soups break down into a fibrous mass meaning that identifying the species of shark that a fin came from is impossible by visual methods. Here, we use molecular techniques to identify the species of sharks found in bowls of soup collected in Singapore. We identified a number of endangered species in the surveyed soups, and many of these species have been shown to contain high levels of mercury, a potent neurotoxin. It is highly likely that consumers of shark fin soup are consuming levels of mercury that are above safe allowable limits, and at the same time are contributing to the massive declines in global shark populations.

Abstract

Shark fin soup, consumed by Asian communities throughout the world, is one of the principal drivers of the demand of shark fins. This near USD 1 billion global industry has contributed to a shark population declines of up to 70%. In an effort to arrest these declines, the trade in several species of sharks is regulated under the auspices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Despite this legal framework, the dried fins of trade-regulated sharks are frequently sold in markets and consumed in shark fin soup. Shark fins found in soups break down into a fibrous mass of ceratotrichia, meaning that identifying the species of sharks in the soup becomes impossible by visual methods. In this paper, we use DNA barcoding to identify the species of sharks found in bowls of shark fin soup collected in Singapore. The most common species identified in our samples was the blue shark (Prionace glauca), a species listed as Near Threatened on the International Union for Conservation of Nature (IUCN) Red List with a decreasing population, on which scientific data suggests catch limits should be imposed. We identified four other shark species that are listed on CITES Appendix II, and in total ten species that are assessed as Critically Endangered, Endangered or Vulnerable under the IUCN Red List of Threatened Species. Globally, the blue shark has been shown to contain levels of mercury that frequently exceed safe dose limits. Given the prevalence of this species in the examined soups and the global nature of the fin trade, it is extremely likely that consumers of shark fin soup will be exposed to unsafe levels of this neurotoxin.