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.

Drones can reliably, accurately and with high levels of precision, collect large volume water samples and physio-chemical data from lakes

The rapid development and application of drone technology has included water sampling and collection of physiochemical data from lakes. Previous research has demonstrated the significant potential of drones to play a future pivotal role in the collection of such data from lakes that fulfil requirements of large-scale monitoring programmes. However, currently the utilisation of drone technology for water quality monitoring is hindered by a number of important limitations: i) the low rate of successful sample captured; ii) the relatively low volume of water sample retrieved for analyses of multiple water chemistry parameters; and critically iii) differences between water chemistry parameters when using a drone versus samples collected by boat. Here we present results comparing the water chemistry results of a large number of parameters (pH, dissolved oxygen concentration, temperature, conductivity, alkalinity, hardness, true colour, chloride, silica, ammonia, total oxidised nitrogen, nitrite, nitrate, ortho-phosphate, total phosphorous and chlorophyll) sampled via drone with samples collected by boat in a number of lakes. The drone water sampling method used here is the first to collect a sufficiently large volume of water to meet the monitoring requirements of large scale water monitoring programmes, 2 L, at a 100% success rate and most crucially, with water chemistry variables that are not significantly different to those taken using traditional boat water sampling. This study therefore shows that drone technology can be utilised to collect water chemistry data and samples from lakes in a reliable, more rapid and cost effective manner than traditional sampling using boats, that is safer for personnel and poses less of a biosecurity risk.

Acid treatment of Atlantic salmon (Salmo salar) scales prior to analysis has negligible effects on δ13C and δ15N isotope ratios

There is debate in the literature as to whether scales of fishes require acidification to remove inorganic carbonates prior to stable isotope analysis. Acid-treated and untreated scales from 208 Atlantic salmon from nine locations on both sides of the Atlantic were analysed for δ13C and δ15N. Linear mixed-effect models determined the effect of acid treatment to be statistically significant. However, the mean difference was small (δ13C 0.1 ± 0.2‰, δ15N -0.1 ± 0.2‰) and not of biological relevance. This study concludes that Atlantic salmon scales do not need to be acidified prior to stable isotope analysis.

Importance of suspended particulate organic matter in the diet of Nephrops norvegicus (Linnaeus, 1758)

The extent to which commercially important Nephrops norvegicus lobsters feed on particulates in the wild is unknown, even though this could be an important way for burrow-dwelling females to avoid starvation during the long breeding season. This was investigated using δ¹³C and δ¹⁵N isotopic signatures in tissues with long and short turnover rates to provide diet discrimination and compare this between males and females. Secondary objectives examined size-related differences and calculated the trophic position based on the new results. Almost half the diet (47%) was made up of suspended particulate organic matter (POM_susp) alone. Fish was another important item in the diet, with plankton and invertebrate sources coming much lower down in dietary importance. Significantly more suspension feeding was observed in small or medium sized individuals than large ones in both sexes. However, there were no sex-related patterns, despite females being restricted to burrows for part of the analysis period. Female diet was almost identical to males and POM_susp comprised a large component of the diet in both sexes. The trophic position was estimated at 2.94 ± 0.16 (mean ± SD), which was at the lower end of the range reported in previous studies (2.60 to 4.32).

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.

Trace element fingerprinting of blue mussel (Mytilus edulis) shells and soft tissues successfully reveals harvesting locations

Globally, aquaculture products are expected to account for >60% of total seafood produce by 2030. In the European Union, the seafood sector is of considerable economic importance to member states with household spending on seafood produce totalling €54.8 billion in 2016. Within the EU, shellfish aquaculture supports livelihoods and employment in many rural communities throughout the region. Harmful algal blooms pose considerable risk to consumer safety and in turn, stability of the shellfish market. If contaminated produce was to make it to the market the health risk to the public could be considerable, but the damage to the sector through loss of trust in producers would also be significant. Mytilus edulis account for a considerable portion of the aquaculture sector in the Northeast Atlantic. At present, no scientific tool is available to industry regulators, to allow them to trace mussel produce to its source, uphold food safety standards and ensure consumer confidence. The present study uses chemical analysis of shells and soft tissues to classify individual M. edulis to their site of harvest. The use of random forest classification of trace element composition has revealed location specific elemental signatures for all examined sites. This led to the correct classification of 100% of individuals sampled to their respective harvesting locations, including two sites located just 6 km apart within the same bay. The protocol demonstrated here provides the basis for a scientifically driven traceability framework for shellfish produce.

Can drones be used to conduct water sampling in aquatic environments? A review

Advancements in drone technology have seen the development of drone-assisted water sampling payloads resulting in the ability of drones to retrieve water samples and physico-chemical data from aquatic ecosystems. The application of drones for water sampling provides the potential to fulfil many aspects of the biological and physico-chemical sampling required to meet large-scale water sampling programmes. This paper reviews the achievements made in the development of drone platforms; advances in specially designed water sampling payloads; advances in incorporating off-the-shelf probes and the ability of drone-assisted water sampling payloads to capture water and physico-chemical data from freshwater environments. However, drone-assisted water sampling is still in its infancy and several key limitations include the small volume of water captured via drones to date, the low rate of successful sample capture and the legislative restrictions limiting the distance drones can be flown from the operator. Of critical importance, however, are the clear inconsistencies observed between water chemical parameters obtained using drone-assisted and traditional water sampling methods. Consequently, water samples and physico-chemical data obtained using drones may not provide the level of reliability and accuracy needed to meet the needs of large-scale water sampling programmes. Solutions aimed at addressing these limitations and developing the potential of drones to conduct water samples include: modifying larger drones with greater payload capacity, facilitating the capture of greater volumes of water; technological developments to increase success rates of water capture; planning fieldwork for operation beyond visual line of sight (BVLOS); employing real-time physico-chemical probes; and integrating robust statistical experimental designs. In addition, detailed cost benefit analyses are required to investigate if drones would result in a meaningful financial saving to water sampling programmes. However, it is envisaged that drone-assisted water sampling will act as a pivotal supporting tool if such current limitations can be addressed by future research.

Stable-isotope analysis reveals the importance of soft-bodied prey in the diet of lesser spotted dogfish Scyliorhinus canicula

This study examines the diet of lesser spotted dogfish Scyliorhinus canicula, one of the most ubiquitous predators of European coastal waters. This species is of increasing ecological significance as other large predatory fish decline as it has known interactions with fisheries. Scyliorhinus canicula diet was investigated in Irish coastal waters during June and July 2014 using both stomach-content analysis and δ¹³ C and δ¹⁵ N stable-isotope ratios. Prey contribution to the diet from dual stable-isotope data was estimated using Bayesian mixing models. It was found that only stable-isotope analysis provided a time-integrated picture of the diet of S. canicula and allowed for a new estimation of their trophic position. Trophic positions from stomach-content analysis within the present study and previous studies were found to be higher than revealed by isotopes. Stomach-content analysis could not reveal the importance of soft-bodied animals in the diet of these fish, however this approach remains a valuable tool to understand the potential prey spectrum in advance of isotope analysis and allows for a better resolution down to species level. The results highlight a greater variety in the diet of this important predator and the benefit of taking a multidisciplinary approach in dietary studies.

Development of non-lethal sampling of carbon and nitrogen stable isotope ratios in salmonids: effects of lipid and inorganic components of fins

The preferred tissue for analyses of fish stable isotope ratios for most researchers is muscle, the sampling of which typically requires the specimen to be sacrificed. The use of non-destructive methods in fish isotopic research has been increasing recently, but as yet is not a standard procedure. Previous studies have reported varying levels of success regarding the utility of non-lethally obtained stable isotope materials, e.g. fins, but none have accounted for the potential compounding effects of inorganic components of fin rays or lipids. Comparisons of carbon (δ(13)C) and nitrogen (δ(15)N) stable isotope ratios of muscle with adipose and caudal fin of two salmonids, Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.), revealed that caudal fin can be used as a non-destructive surrogate for muscle in stable isotope analysis, but that adipose fin, where available, is a better proxy. The use of a published model to inexpensively counteract the confounding effect of lipids, which are depleted in (13)C, greatly improved the relationship between fish muscle and fins. However, efforts to account for the inorganic components of fin rays were counterproductive and required twice the biomass of fins clipped from each fish. As this experiment was conducted on wild fish, controlled laboratory studies are required to confirm these field observations.

The impact of catchment conifer plantation forestry on the hydrochemistry of peatland lakes

The hydrochemistry of 26 small blanket bog lakes was examined to assess the impact of conifer plantation forestry on lake water chemistry. Lakes were selected from three distinct catchment land use categories: i) unplanted blanket bog only present in the catchment, ii) mature (closed-canopy) conifer plantation forests only present in the catchment and iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sedimentary (sandstone) and igneous (granite). Lakes with afforested catchments across both geologies had elevated concentrations of phosphorus (P), nitrogen (N), total dissolved organic carbon (TDOC), aluminium (Al) and iron (Fe), with the highest concentrations of each parameter recorded from lakes with catchment clearfelling. Dissolved oxygen was also significantly reduced in the afforested lakes, particularly the clearfell lakes. Analysis of runoff from a nearby recently clearfelled site revealed high biological and chemical oxygen demands, consistent with at least part of the elevated concentrations of TDOC emanating from clearfelled sites having higher biochemical lability. Inorganic fertilisers applied at the start of the forest cycle, the decay of the underlying peat soil and accumulated surface tree litter, and leachate from felled trees are the likely sources of the elevated concentrations of plant nutrients, TDOC, heavy metals and major ions, with excessive peat soil disturbance during clearfelling likely exacerbating the runoff into lakes. Our study has demonstrated a clear, deleterious impact of conifer plantations on the water quality draining from blanket bog catchments, with major implications for the management of afforested peatlands.

Implications of climate change for the fishes of the British Isles

Recent climatic change has been recorded across the globe. Although environmental change is a characteristic feature of life on Earth and has played a major role in the evolution and global distribution of biodiversity, predicted future rates of climatic change, especially in temperature, are such that they will exceed any that has occurred over recent geological time. Climate change is considered as a key threat to biodiversity and to the structure and function of ecosystems that may already be subject to significant anthropogenic stress. The current understanding of climate change and its likely consequences for the fishes of Britain and Ireland and the surrounding seas are reviewed through a series of case studies detailing the likely response of several marine, diadromous and freshwater fishes to climate change. Changes in climate, and in particular, temperature have and will continue to affect fish at all levels of biological organization: cellular, individual, population, species, community and ecosystem, influencing physiological and ecological processes in a number of direct, indirect and complex ways. The response of fishes and of other aquatic taxa will vary according to their tolerances and life stage and are complex and difficult to predict. Fishes may respond directly to climate-change-related shifts in environmental processes or indirectly to other influences, such as community-level interactions with other taxa. However, the ability to adapt to the predicted changes in climate will vary between species and between habitats and there will be winners and losers. In marine habitats, recent changes in fish community structure will continue as fishes shift their distributions relative to their temperature preferences. This may lead to the loss of some economically important cold-adapted species such as Gadus morhua and Clupea harengus from some areas around Britain and Ireland, and the establishment of some new, warm-adapted species. Increased temperatures are likely to favour cool-adapted (e.g. Perca fluviatilis) and warm-adapted freshwater fishes (e.g. roach Rutilus rutilus and other cyprinids) whose distribution and reproductive success may currently be constrained by temperature rather than by cold-adapted species (e.g. salmonids). Species that occur in Britain and Ireland that are at the edge of their distribution will be most affected, both negatively and positively. Populations of conservation importance (e.g.Salvelinus alpinus and Coregonus spp.) may decline irreversibly. However, changes in food-web dynamics and physiological adaptation, for example because of climate change, may obscure or alter predicted responses. The residual inertia in climate systems is such that even a complete cessation in emissions would still leave fishes exposed to continued climate change for at least half a century. Hence, regardless of the success or failure of programmes aimed at curbing climate change, major changes in fish communities can be expected over the next 50 years with a concomitant need to adapt management strategies accordingly.

The effects of the levonorgestrel intrauterine system (Mirena coil) on endometrial morphology

AIMS

The Mirena coil is a levonorgestrel releasing intrauterine device that is in widespread use. This study aims to document the endometrial morphology associated with this device.

METHODS

Endometrial specimens from 75 women with the Mirena coil were reviewed and the histological features detailed.

RESULTS

Morphological features found in most of the endometria were decidualisation of stroma (72 of 75 cases), atrophy of endometrial glands (65 of 75 cases), a surface papillary pattern (38 of 75 cases), and a stromal inflammatory cell infiltrate (59 of 75 cases). Additional common histological features were the presence of foci of stromal myxoid change (29 of 75 cases) and stromal haemosiderin pigment (24 of 75 cases). Reactive atypia of surface glands, glandular metaplastic changes, stromal necrosis, and stromal calcifications were found in small numbers of cases.

CONCLUSION

The endometrial features are characteristic and relatively constant and are in keeping with the effects of both a progestogenic compound and a mechanical device. Pathologists should be aware of these histological features because the Mirena coil is in widespread use.

Pleomorphic lipoma of the parotid gland

Lipomata are rare tumours of the parotid gland. The pleomorphic lipoma represents an unusual histological variant of the benign lipoma. We report a case of a pleomorphic lipoma arising in the parotid gland. Only one case of a similar nature has previously been recorded. This tumour is benign, was fully excised and recurrence is not expected.

Growth hormone secreting pituitary carcinoma: a case report and literature review

Only five cases of growth hormone secreting pituitary carcinoma have been documented. We present a 49-year-old West Indian male with grossly elevated plasma growth hormone (760-10,400 mU/l), and a large aggressive pituitary tumour that continued to grow despite repeated pituitary surgery, radiotherapy and medical therapy (bromocriptine and somatostatin analogue). Thirteen years after diagnosis the patient died secondary to left ventricular failure. A post-mortem revealed a large locally invasive pituitary tumour, but in addition numerous tumour seedlings within the cerebrospinal fluid space, and a solitary intraparenchymal tumour deposit within the right temporal lobe, clearly separate from the primary tumour. Pituitary carcinoma should be considered in any acromegalic with grossly elevated plasma growth hormone levels who fails to respond to conventional therapy.