Shark-dust: Application of high-throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g., fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity, and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, and are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded “shark-dust” samples from seven processing plants in the world's biggest shark landing site (Java, Indonesia), and identified 61 shark and ray taxa (representing half of all chondrichthyan orders), more than half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding.

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access

Shark and ray trade in and out of Indonesia: Addressing knowledge gaps on the path to sustainability

Indonesian marine resources are among the richest on the planet, sustaining highly diverse fisheries. These fisheries include the largest shark and ray landings in the world, making Indonesia one of the world’s largest exporters of elasmobranch products. Socio-economic and food security considerations pertaining to Indonesian communities add further layers of complexity to the management and conservation of these vulnerable species. This study investigates the elasmobranch trade flows in and out of Indonesia and attempts to examine patterns and drivers of the current scenario. We identify substantial discrepancies between reported landings and declared exports, and between Indonesian exports in elasmobranch fin and meat products and the corresponding figures reported by importing countries. These mismatches are estimated to amount to over $43.6 M and$20.9 M for fins and meat, respectively, for the period between 2012 and 2018. Although the declared exports are likely to be an underestimation because of significant unreported or illegal trading activities, we note that domestic consumption of shark and ray products may also explain these discrepancies. The study also unearths a general scenario of unsystematic data collection and lack of granularity of product terminology, which is inadequate to meet the challenges of over-exploitation, illegal trade and food security in Indonesia. We discuss how to improve data transparency to support trade regulations and governance actions, by improving inspection measures, and conserving elasmobranch populations without neglecting the socio-economic dimension of this complex system

Seasonal development of a tidal mixing front drives shifts in community structure and diversity of bacterioplankton

Bacterioplankton underpin biogeochemical cycles and an improved understanding of the patterns and drivers of variability in their distribution is needed to determine their wider functioning and importance. Sharp environmental gradients and dispersal barriers associated with ocean fronts are emerging as key determinants of bacterioplankton biodiversity patterns. We examined how the development of the Celtic Sea Front (CF), a tidal mixing front on the Northwest European Shelf affects bacterioplankton communities. We performed 16S-rRNA metabarcoding on 60 seawater samples collected from three depths (surface, 20 m and seafloor), across two research cruises (May and September 2018), encompassing the intra-annual range of the CF intensity. Communities above the thermocline of stratified frontal waters were clearly differentiated and less diverse than those below the thermocline and communities in the well-mixed waters of the Irish Sea. This effect was much more pronounced in September, when the CF was at its peak intensity. The stratified zone likely represents a stressful environment for bacterioplankton due to a combination of high temperatures and low nutrients, which fewer taxa can tolerate. Much of the observed variation was driven by Synechococcus spp. (cyanobacteria), which were more abundant within the stratified zone and are known to thrive in warm oligotrophic waters. Synechococcus spp. are key contributors to global primary productivity and carbon cycling and, as such, variability driven by the CF is likely to influence regional biogeochemical processes. However, further studies are required to explicitly link shifts in community structure to function and quantify their wider importance to pelagic ecosystems

Resource competition drives an invasion-replacement event among shrew species on an island

Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural ‘control’ site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services

Oxygen Tension Is a Determinant of the Matrix-Forming Phenotype of Cultured Human Meniscal Fibrochondrocytes

BACKGROUND: Meniscal cartilage displays a poor repair capacity, especially when injury is located in the avascular region of the tissue. Cell-based tissue engineering strategies to generate functional meniscus substitutes is a promising approach to treat meniscus injuries. Meniscus fibrochondrocytes (MFC) can be used in this approach. However, MFC are unable to retain their phenotype when expanded in culture. In this study, we explored the effect of oxygen tension on MFC expansion and on their matrix-forming phenotype. METHODOLOGY/PRINCIPAL FINDINGS: MFC were isolated from human menisci followed by basic fibroblast growth factor (FGF-2) mediated cell expansion in monolayer culture under normoxia (21%O(2)) or hypoxia (3%O(2)). Normoxia and hypoxia expanded MFC were seeded on to a collagen scaffold. The MFC seeded scaffolds (constructs) were cultured in a serum free chondrogenic medium for 3 weeks under normoxia and hypoxia. Constructs containing normoxia-expanded MFC were subsequently cultured under normoxia while those formed from hypoxia-expanded MFC were subsequently cultured under hypoxia. After 3 weeks of in vitro culture, the constructs were assessed biochemically, histologically and for gene expression via real-time reverse transcription-PCR assays. The results showed that constructs under normoxia produced a matrix with enhanced mRNA ratio (3.5-fold higher; p<0.001) of collagen type II to I. This was confirmed by enhanced deposition of collagen II using immuno-histochemistry. Furthermore, the constructs under hypoxia produced a matrix with higher mRNA ratio of aggrecan to versican (3.5-fold, p<0.05). However, both constructs had the same capacity to produce a glycosaminoglycan (GAG) -specific extracellular matrix. CONCLUSIONS: Our data provide evidence that oxygen tension is a key player in determining the matrix phenotype of cultured MFC. These findings suggest that the use of normal and low oxygen tension during MFC expansion and subsequent neo-tissue formation cultures may be important in engineering different regions of the meniscus

Geographical Representativeness of Published and Ongoing Randomized Controlled Trials. The Example of: Tobacco Consumption and HIV Infection

BACKGROUND: The challenge for evidence-based healthcare is to reduce mortality and the burden of diseases. This study aimed to compare where research is conducted to where research is needed for 2 public health priorities: tobacco consumption and HIV infection. METHODS: We identified randomized controlled trials (RCTs) included in Cochrane systematic reviews published between 1997 and 2007 and registered ongoing RCTs identified in January 2009 through the World Health Organization's International Clinical Trials Registry Platform (WHO-ICTRP) evaluating interventions aimed at reducing or stopping tobacco use and treating or preventing HIV infection. We used the WHO and World Bank reports to classify the countries by income level, as well as map the global burden of disease and mortality attributable to tobacco use and HIV infection to the countries where the trials performed. RESULTS: We evaluated 740 RCTs included in systematic reviews and 346 ongoing RCTs. For tobacco use, 4% of RCTs included in systematic reviews and 2% of ongoing trials were performed in low- and middle-income countries, even though these countries represented 70% of the mortality related to tobacco use. For HIV infection, 31% of RCTs included in systematic reviews and 33% of ongoing trials were performed in low- and middle-income countries, even though these countries represented 99% of the mortality related to HIV infection. CONCLUSIONS: Our results highlight an important underrepresentation of low- and middle-income countries in currently available evidence (RCTs included in systematic reviews) and awaiting evidence (registered ongoing RCTs) for reducing or stopping tobacco use and treating or preventing HIV infection

Tests of multiple molecular markers for the identification of Great Spotted and Syrian Woodpeckers and their hybrids

Great Spotted and Syrian Woodpeckers (Dendrocopos major and D. syriacus) are known to hybridize in nature; however, the extent of this phenomenon is not known due to difficulties in hybrid detection based on plumage analyses. Here, we tested five markers (one mitochondrial and four nuclear) and a set of six microsatellite loci for the identification of these two Woodpeckers and their hybrids. Sequencing of DNA from 26 individuals of both Woodpeckers from different parts of their ranges: one allopatric (D. major; Norway) and two sympatric (Poland and Bulgaria) showed that both species can be clearly separated based on all sequence markers. The highest number of fixed nucleotide sites were found in the mtDNA control region and intron 5 of the transforming growth factor. Analyses of microsatellite data distinguished the two species, but all loci showed a large number of common alleles and their utility in identifying hybrids is therefore doubtful. According to the DNA sequence analyses, 2 out of 18 specimens within the sympatric range in Poland were identified as possible hybrids, most probably paternal backcrosses. Moreover, both hybrids are from synantropic populations (settled in cities), whereas none of the D. major sampled in forests and in its allopatric range (Norway) showed signs of an intermixed genotype. Further research on hybridization and introgression in woodpeckers is undoubtedly needed and could be useful for understanding ecological and ethological interactions among these species, particularly for D. syriacus, which is relatively rare in Europe

UK DNA working group eDNA week, January 2022

Here, we report on eDNA week, an international conference held online as a five-day series of webinars from January 17, 2022, to January 21, 2022. The conference was organized by the UK DNA working group, which has witnessed considerable growth and application of eDNA research since its founding and first conference in 2014. The 2022 event, held online due to the COVID-19 pandemic, provided an opportunity to invite international researchers who are leading the field, without the usual constraints of conference location. Compared with the previous UK-based in-person conferences, there was greater international participation amongst the 514 people who registered to attend the event. To emphasize the importance of collaboration between sectors in driving forward DNA monitoring, a session was devoted to presentations by participants from governmental agencies, and another to those from commercial companies developing and utilizing DNA tools. The industry and stakeholder sessions were accompanied by state-of-the-art presentations delivered by a global group of DNA/eDNA researchers from 11 countries. These sessions were complemented by an open forum session for reflection and discussion