A simple one-step PCR method for the identification between European and American razor clams species

Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species

Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.

Essential and Non-Essential Elements in Razor Clams (Solen marginatus, Pulteney, 1799) from the Domitio Littoral in Campania (Southwestern Tyrrhenian Sea, Italy)

The levels of essential (Cu, Cr, Co, Mn, Se, Zn) and non-essential (As, Be, Bi, Cd, Cs, Ga, Ni, Pb, Sr, Tl, U, V) trace elements were studied in razor clams (Solen marginatus) collected from the Tyrrhenian coast of Southern Italy at five selected sites along the Domitio littoral in the Campania region. The main objectives of this study were to assess the contamination status of these bivalve mollusks and to evaluate the risks to the environment and consumers due to metal contamination. The concentrations of 18 trace elements were determined after microwave-assisted mineralization and by inductively coupled plasma mass spectrometry (ICP-MS). Concentrations of the toxic elements Pb and Cd were below the maximum levels established by Commission Regulation (EC) 1881/2006, while higher average concentrations of arsenic were found at each of the five sites studied. Regarding the other trace elements, contamination levels followed the order: Zn > Sr > Mn > Cu > Se > Cr > V > Ni > Co > Ga > Cs > Be > U > Bi > Tl. No significant differences among the sites were found with regard to any of the trace elements analyzed, and element levels in razor clams did not reflect sediment contamination. The results demonstrated the substantial food safety of the razor clams in this area with respect to heavy metals but revealed a potential health risk due to arsenic contamination in all the areas sampled.

Spatio-temporal trace element fingerprinting of king scallops (Pecten maximus) reveals harvesting period and location

A rapidly growing human population is increasingly relying on seafood as a source of protein and other essential nutrients. Bivalve shellfish, both from wild populations and aquaculture, will undoubtedly continue to account for a significant portion of overall seafood production, but consumption of such shellfish carries potential health risks. Biotoxins, disease causing organisms and pollution contribute to this risk, as shellfish are indiscriminate, passive filter feeders. While government bodies, industry regulators and producers are capable of managing this risk, counterfeit produce can risk public safety, in turn damaging the reputation of the entire industry. Traceability tools provide a means to uphold food safety standards and mitigate remaining risk to consumers. Here, we show how the use of trace element (TE) signatures in shells and soft tissues of king scallops combined, can predict geographic origin with 100% accuracy. Importantly, we explore the temporal stability of this method, successfully classifying 100% of individuals correctly between two dates just 42 days apart from the same harvesting location. The most important elements in the trace element signatures of the scallops, discriminating between harvesting sites and dates were barium, boron, chromium, lead, manganese, molybdenum and selenium. The traceability tool described here offers a viable method to trace produce to its source, empowering industry regulators, government authorities, aquaculture practitioners and retailers in terms of tracking shellfish throughout the supply chain, which would comply with legislation and boost consumer confidence.

Lab-on-a-Chip-Based PCR-RFLP Assay for the Detection of Malayan Box Turtle (Cuora amboinensis) in the Food Chain and Traditional Chinese Medicines

The Malayan box turtle (Cuora amboinensis) (MBT) is a vulnerable and protected turtle species, but it is a lucrative item in the illegal wildlife trade because of its great appeal as an exotic food item and in traditional medicine. Although several polymerase chain reaction (PCR) assays to identify MBT by various routes have been documented, their applicability for forensic authentication remains inconclusive due to the long length of the amplicon targets, which are easily broken down by natural decomposition, environmental stresses or physiochemical treatments during food processing. To address this research gap, we developed, for the first time, a species-specific PCR-restriction fragment length polymorphism (RFLP) assay with a very short target length (120 bp) to detect MBT in the food chain; this authentication ensured better security and reliability through molecular fingerprints. The PCR-amplified product was digested with Bfa1 endonuclease, and distinctive restriction fingerprints (72, 43 and 5 bp) for MBT were found upon separation in a microfluidic chip-based automated electrophoresis system, which enhances the resolution of short oligos. The chances of any false negative identifications were eliminated through the use of a universal endogenous control for eukaryotes, and the limit of detection was 0.0001 ng DNA or 0.01% of the meat under admixed states. Finally, the optimized PCR-RFLP assay was validated for the screening of raw and processed commercial meatballs, burgers and frankfurters, which are very popular in most countries. The optimized PCR-RFLP assay was further used to screen MBT materials in 153 traditional Chinese medicines of 17 different brands and 62 of them were found MBT positive; wherein the ingredients were not declared in product labels. Overall, the novel assay demonstrated sufficient merit for use in any forensic and/or archaeological authentication of MBT, even under a state of decomposition.

Trace element fingerprinting of cockle (Cerastoderma edule) shells can reveal harvesting location in adjacent areas

Determining seafood geographic origin is critical for controlling its quality and safeguarding the interest of consumers. Here, we use trace element fingerprinting (TEF) of bivalve shells to discriminate the geographic origin of specimens. Barium (Ba), manganese (Mn), magnesium (Mg), strontium (Sr) and lead (Pb) were quantified in cockle shells (Cerastoderma edule) captured with two fishing methods (by hand and by hand-raking) and from five adjacent fishing locations within an estuarine system (Ria de Aveiro, Portugal). Results suggest no differences in TEF of cockle shells captured by hand or by hand-raking, thus confirming that metal rakes do not act as a potential source of metal contamination that could somehow bias TEF results. In contrast, significant differences were recorded among locations for all trace elements analysed. A Canonical Analysis of Principal Coordinates (CAP) revealed that 92% of the samples could be successfully classified according to their fishing location using TEF. We show that TEF can be an accurate, fast and reliable method to determine the geographic origin of bivalves, even among locations separated less than 1 km apart within the same estuarine system. Nonetheless, follow up studies are needed to determine if TEF can reliably discriminate between bivalves originating from different ecosystems.

Effect of coastal eutrophication on heavy metal bioaccumulation and oral bioavailability in the razor clam, Sinonovacula constricta

As traditional seafoods, the razor clams are widely distributed from tropical to temperate areas. Coastal razor clams are often exposed to eutrophication. Heavy metal contamination is critical for seafood safety. However, how eutrophication affects bioaccumulation and oral bioavailability of heavy metals in the razor clams is unknown. After a four-month field experimental cultivation, heavy metals (Fe, Cu, Ni, V, As, and Pb) could be bioaccumulated by the razor clams (Sinonovacula constricta) through exposure to metals present in water and sediments or in the food chain, and then transferred to human via consumption of razor clams. Bionic gastrointestinal digestion and monolayer liposome extraction are used for metal oral bioavailability (OBA) assessment. The influence of eutrophication on OBA is decreased for Fe and Pb and increased for V. A significant positive linear correlation was observed between the bioaccumulation factors of Fe, Ni, V, and As in razor clams and the coastal eutrophication. These results may be due to the effect of eutrophication on metal species transformation in coastal seawater and subcellular distribution in razor clams. The maximum allowable daily intakes of razor clams are controlled by eutrophication status and the concentration of affinity-liposome As in razor clams.

Advances in DNA-based techniques for the detection of seafood species substitution on the commercial market

Increased worldwide trade and processing of seafood has increased the potential for species substitution on the commercial market. To detect and prevent species substitution, several deoxyribonucleic acid (DNA)-based methods have been developed that can be used to identify species in a variety of food types. For large-scale applications, such as regulatory screening, these methods must be rapid, cost-effective, reliable, and have high potential for automation. This review highlights recent technological advances in DNA-based identification methods, with a focus on seafood species identification in automated, high-throughput settings. Advances in DNA isolation methods include silica-based columns for use in high-throughput operations and magnetic bead particles for increased and targeted recovery of DNA. The three most widely used methods for seafood species identification (polymerase chain reaction [PCR] sequencing, PCR-restriction fragment length polymorphism, and species-specific PCR) will be discussed, with a focus on the incorporation of technologies such as rapid PCR cycling, microfluidic chips, and real-time PCR. Emerging methods, including DNA microarrays and next-generation sequencing will also be explored for their potential to identify seafood species on a large scale. Overall, many of the technological advances discussed here offer complementary properties that will enable species identification in a variety of settings and with a range of products.