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.

Deep Sea Microplastic Pollution Extends Out to Sediments in the Northeast Atlantic Ocean Margins

Microplastics are ubiquitous emerging contaminants found in every habitat surveyed, building upon international databases globally. Costs and accessibility often correlate to few deep sea sediment surveys, restricting the number of stations within a given sampling area. An extensive survey of the Porcupine Seabight, Porcupine Bank, the Goban Spur, and south-western canyons resulted in identifying microplastics in deep sea sediment surface layers from 33 of the 44 stations sampled (75%), with a total of 83 particles (74 synthetic and 9 natural) recorded. No microplastic hotspots were identified, and abundances (kg d.w.^-1) were not correlated with distance from land, depth, or the presence of macrolitter on the seafloor. Understanding the sources of deep sea microplastics, such as marine traffic, is crucial to developing effective mitigation strategies as well as further monitoring campaigns targeting microplastic pollution in areas with significant deep sea biodiversity such as the Porcupine Seabright.

Size dependent egestion of polyester fibres in the Dublin Bay Prawn (Nephrops norvegicus)

Microplastics (MPs) are an extensive global contaminant in the marine environment, known to be ingested by marine organisms. The presence of MPs in the commercially important marine decapod crustacean Nephrops norvegicus (Dublin Bay Prawn) has been documented for the North-East Atlantic and the Mediterranean, however, uncertainties remain about retention times of MPs in the gastrointestinal tract (GIT) of this species. This study aims to investigate the retention times of polyester MP fibres of three sizes (3, 5, and 10 mm in length) and to determine whether the egestion of MP fibres is size and time dependent. Results suggest that MP fibres of different lengths are retained for different periods of time, with larger MP fibres being retained for longer periods (e.g., minimum 96 h for 10 mm fibres). The present study also assesses for the first time, the size dependent relationship of MP fibres under controlled conditions for N. norvegicus.

Plastics, prawns, and patterns: Microplastic loadings in Nephrops norvegicus and surrounding habitat in the North East Atlantic

The presence of microplastics (MPs), a contaminant of emerging concern, has attracted increasing attention in commercially important seafood species such as Nephrops norvegicus. This species lend themselves well as bioindicators of environmental contamination owing to their availability, spatial and depth distribution, interactions with seafloor sediment and position in the ecosystem and food chain. This study assesses the abundance of MPs in N. norvegicus and in benthic sediments across six functional units in the North East Atlantic. Assessment of the relationship between MP abundance in N. norvegicus, their biological parameters and their surrounding environment was examined. Despite the lack of statistical significance, MP abundances, size, shape, and polymer type recorded in N. norvegicus mirrored those found in the surrounding environment samples. The three main polymers identified in both organisms and sediment were polystyrene, polyamide (nylons), and polypropylene. The level of MP contamination in N. norvegicus could be related to local sources, with relatively low abundances recorded in this study for the North East Atlantic in comparison to other regional studies. Furthermore, larger organisms contained a lower abundance of MPs, demonstrating no accumulation of MPs in N. norvegicus. Based on the results of this study, data on MP ingestion could be used to study trends in the amount and composition of litter ingested by marine animals towards fulfilling requirements of descriptor 10 of the Marine Strategy Framework Directive.

Assessing microplastic distribution within infaunal benthic communities in a coastal embayment

Marine anthropogenic litter is increasing in prevalence in both the marine environment and its inhabitants. This study assesses the levels of anthropogenic microplastics in benthic infauna from 20 subtidal stations in Galway Bay, Ireland. Microplastics were removed from the organisms using an alkaline digestion (KOH) and their synthetic origin was confirmed by μFTIR spectroscopic analysis. The average number of microplastics recorded for all organisms was 0.79 ± 1.14 particles individual^-1, similar to previously published results on subtidal fauna of the North Sea. Fibres were the dominant particle type (98%) and the majority were identified as natural (cellulose, cotton). Synthetic polymers identified included PVA (polyvinyl acetate), EPDM (synthetic rubber), PE (polyethylene) and PVC (polyvinyl chloride). Fibres less than 1 mm made up 55% of the recovered lengths. Colours recorded in the organisms were mainly blue and were reflective of the surrounding habitats. Of the five phyla collected, the highest incidence and uptake was associated with the Annelida. A significant difference in ingested MPs was only evident when depth (greater and less than 30 m) was considered as a factor. In addition, no significant differences were found between either the numbers of ingested MPs and phyla or feeding strategies. The results indicate that future studies should follow an ecosystem-based approach to monitor MPs levels in an area where specific bioindicator(s) have not been identified or are unsuitable.

Differences in microplastic abundances within demersal communities highlight the importance of an ecosystem-based approach to microplastic monitoring

Plastic pollution is prevalent in all habitats and microplastic ingestion has been recorded in several different species examined to date. However, most studies have focused solely on commercial species. This study investigates microplastics (MPs) by assessing the levels present in a mixed demersal trawl at two sites in a coastal embayment. MPs were recovered from species' gastrointestinal tracts and polymers identified with μFTIR spectroscopic analysis. Particles recovered comprised 20% natural fibres. The majority of MPs were identified as PE, PVDF, and PETE. Results show an average MP range of 0.11-4.67 MPs individual^-1. Fluctuating trendlines for MPs within species suggest that their bioavailability is influenced by several factors. Individual species show significant differences in ingested MP between trawls; however, when the entire trawl community is assessed there is no significant difference between sites. These results suggest that future studies should follow an ecosystem-based approach to monitor MPs.

Learning styles of deaf college students and instructors' teaching emphases

Six learning style dimensions of the Grasha-Riechmann Student Learning Style Scales (GRSLSS) were examined in this study with 100 deaf college students. In addition, six corresponding scales of teaching emphases were administered to the 16 instructors of these students. Student mean scores were higher for the dependent, participative, collaborative, and independent dimensions than for the competitive and avoidant styles. The participative learning style correlated significantly with course achievement and course interest, which suggests that an emphasis on active learning may be desirable. For instructors, as with students, the mean scores for teaching emphases were found to be higher for the collaborative, dependent, participative, and independent dimensions. the similar patterns of results for students and teachers suggest a correspondence between the learning styles and the teaching emphases.

The influence of genetic counselling in the era of DNA testing on knowledge, reproductive intentions and psychological wellbeing

Subjects of reproductive age at risk of having an affected child with a severe single gene disorder such as Duchenne muscular dystrophy (DMD) or cystic fibrosis (CF) were surveyed to ascertain: their views on genetic counselling and antenatal testing; their knowledge of their risk of having an affected child; and their psychological wellbeing. Questionnaires were posted to 209 individuals at 130 addresses; a 65% response rate was achieved. The majority of those surveyed were under 40 years of age (91%), half of them had received genetic counselling only once and for 47% the first encounter was after the diagnosis of their affected child. Most patients expressed their intention to use prenatal testing. However, less than 50% of those counselled knew their risk of having an affected child. Knowledge of risk was associated with the type of disease in the family (p < 0.001) (inheritance of DMD was poorly understood by relevant subjects) and was positively associated with the participant's level of education (p < 0.05). We did not detect a significant association between the number of intended children and the risk of having an affected child. In terms of family relations, genetic counselling appears to be beneficial for the nuclear family, the couple and their children, but some counselees reported a deterioration in relations with other relatives. The results indicate that couples at risk of having a child with a severe genetic disorder value the counselling provided, but many of them do not remember important facts in relation to their risk status.

Microbiological assays for antibiotics and vitamins: considerations for assuring accuracy

Factors that may influence the accuracy and precision of microbiological manual and semiautomated turbidimetric methods as well as diffusion assays are discussed. Influence of kind of equipment, media, test bacteria, sample preparation, form of dose response lines, operations, and personnel on quality of assays is examined with the objective of reducing to insignificance those factors under control of the analyst that are responsible for low quality assays.

Possibility for error in FDA diffusion assays

Computational procedures specified for the FDA single-dose diffusion assay for antibiotics may cause substantial error in estimated sample potency. An unrecognized mistake in reference solution concentration is the source of error. It is caused by correcting responses from standard and sample plates differently. The error can be avoided by correcting both standard and sample responses to the observed reference response.

Microbiological turbidimetric methods: linearization of antibiotic and vitamin standard curves

Procedures were devised to linearize the usually curved calibration lines for turbidimetric microbiological assays. Three new equations relating concentration of drug and turbidity are described; two are for antibiotic assays and one for vitamin assays. One equation is for antibiotic assays employing Klebsiella pneumoniae as the test organism. The accuracy of interpolation from the three equations was studied by means of appropriate mathematical models based on erthromycin, chlortetracycline (K. pneumoniae), and cyanocobalamin assays. The accuracy of the new expressions was significantly superior to those used previously, and they are of general applicability.

Microbiological diffusion assay II: design and applications

Application of new equipment and new techniques was made to antibiotic diffusion assays. Accumulation of data and computation of potencies were made by an on-line computer. The system was tested by assaying cephalexin with the aid of Bacillus subtilis in an FDA single-dose design modified by reducing the number of standards to two. The influence of the thickness of the base layer and the form of the dose-response line were tested. Zone diameter was measured with a resolution of 0.01 mm. The potency of samples was measured with an error usually less than 3%. An error of 0.1 mm in measuring zone size would cause an error of 3% of potency. The usual calibration line was inadequate for extrapolation beyond a twofold range. A dose-response line derived from the Cooper equation was better for standard curves spanning more than a twofold range of concentrations. Precision was better on the plates with the 20-ml base layer. The two-dose method of assaying gave larger errors than the single-dose method. Large variances in measuring zone diameters are a reason for the low precision of diffusion assays and set an inherent limit on precision.

Automated system for analytical microbiology V: calibration lines for antibiotics

The accuracy of an automated system for the microbiological assay of antibiotics was increased by improvement attendant to connection to an on-line computer. The system was used to investigate the suitability of four forms of interpolation formulas by assaying for chlortetracycline and erythromycin. The calibration lines were prepared as point-to-point straight-line approximations and as cubic equations. Cubic equations through four calibration points were preferred. Since the automated system was a four-channel instrument, a separate response line was prepared for each channel. Combining the four response lines into one could substantially degrade the accuracy and precision of assays. A new general equation relating the response of the test organism to concentrations of active materials was used to account for factors in addition to the antibiotic upon the dose-response line. Some of these factors were: diluents, growth substances, relative proportions of mixed antibiotics, pH and buffer capacities of the sample solution and assay broth, salts, and organic compounds in samples and not in standard solutions. The equation was used to show under what conditions the dose-response lines of mixtures and single-component antibiotics could be the same. It could also account for the nonspecific nature of turbidimetric assays. The equation showed assay biases to be caused not by differences in composition of antibiotics in standards and samples but by differences in other substances affecting growth of the test organism. A new dose-response line applicable to assays using Klebsiella pneumoniae was described.

Turbidimetric assays: the antibiotic dose-response line

Several antibiotics reduced growth of bacteria without killing them when present in the range of concentrations of significance in assaying. The reduction in growth rate was linearly related to concentration of antibiotic. From this fact may be derived an equation of the form log N = A - BC where N is the concentration of bacteria at the end of the incubation period, C is the concentration of antibiotic, and A and B are constants. This equation is used to guide the selection of the best range of concentrations of unknown for assay and to show the large influence of variations of temperature upon an assay.

INTERMEDIATES OF VITAMIN B(1) AND THE GROWTH OF TORULA

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