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Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

Aquaculture, as a means of food production, is growing rapidly in response to an increasing demand for protein and the over-exploitation of wild fisheries. This expansion includes mussels (family Mytilidae) where production currently stands at 1.5 million tonnes per annum. Mussel culture is frequently perceived as having little environmental impact yet mussel biodeposits and shell debris accumulate around the production site and are linked to changes in the benthos. To assess the extent and nature of changes in benthos associated with mussel farming grab and video sampling around seven mussel farms was conducted. Grab samples were analysed for macrofauna and shell-hash content whilst starfish were counted and the shell-hash cover estimated from video imaging. Shell-hash was patchily distributed and occasionally dominated sediments (maximum of 2116 g per 0.1 m(2) grab). Mean shell-hash content decreased rapidly at distances >5 m from the line and, over the distance 1-64 m, decreased by three orders of magnitude. The presence of shell-hash and the distance-from-line influenced macrofaunal assemblages but this effect differed between sites. There was no evidence that mussel farming was associated with changes in macrobenthic diversity, species count or feeding strategy. However, total macrofaunal count was estimated to be 2.5 times higher in close proximity to the lines, compared with 64 m distance, and there was evidence that this effect was conditional on the presence of shell-hash. Starfish density varied considerably between sites but, overall, they were approximately 10 times as abundant close to the mussel-lines compared with 64 m distance. There was no evidence that starfish were more abundant in the presence of shell-hash visible on the sediment surface. In terms of farm-scale benthic impacts these data suggest that mussel farming is a relatively benign way of producing food, compared with intensive fish-farming, in similar environments.

The marine aquaculture industry and regulators are in the process of implementing environmental DNA (eDNA) metabarcoding of microbial communities for compliance monitoring. This requires standardization of sampling, laboratory, and data analysis protocols. Towards this goal, we in this study completed two further milestones using samples collected from two Scottish salmon farms: (i) We tested the effect of using two different PCR protocols (i.e., different DNA polymerases, master mixes, and annealing temperatures), which are frequently being used in eDNA biomonitoring of aquaculture installations, for the amplification of the taxonomic marker gene (V3‐V4 hypervariable region of the bacterial 16S rRNA gene). (ii) We quantified sampling background noise obtained from eDNA samples and statistically compared results with the sampling bias observed in macrofaunal samples from the same source sediments. We detected differences in bacterial community structures resulting from the performance of different PCR protocols, profoundly influencing the interpretation of biomonitoring results. Furthermore, we found that sampling‐induced errors for eDNA samples were similar to errors for macrofaunal samples collected according to compliance monitoring protocol (~25% variability in both cases). Finally, we showed that within‐grab variances of microbial community structures were in the same order of magnitude (less than 10× difference in all cases) as the one obtained from replicate grabs collected from the same locale (impact category). Based on our findings, we suggest using a consistent PCR protocol for biomonitoring efforts to improve the comparability of results, especially when different service providers are conducting the biomonitoring. We propose a sampling scheme to be considered in eDNA biomonitoring that includes taking three replicate grabs at each locale, with one replicate sample from each grab. This minimizes sampling‐induced errors and makes upcoming eDNA‐based monitoring results comparable with previous compliance monitoring results obtained from macrofaunal data. We completed two further milestones toward a standardized protocol that is necessary for achieving reliable, reproducible, and efficient results in eDNA‐based biomonitoring of marine coastal aquaculture impacts: this regards (i) the importance of the PCR protocol and (ii) the (replicate) sampling design to minimize noise and maximize information at high cost‐efficiency.

Novel hard substratum, introduced through offshore developments, can provide habitat for marine species and thereby function as an artificial reef. To predict the ecological consequences of deploying offshore infrastructure, and sustainably manage the installation of new structures, interactions between artificial reefs and marine ecosystem functions and services must be understood. This requires quantitative data on the relationships between secondary productivity and artificial reef design, across all trophic levels. Benthic secondary productivity is, however, one of the least studied processes on artificial reefs. In this study, we show that productivity rates of a common suspension feeder, Flustra foliacea (Linnaeus 1758), were 2.4 times higher on artificial reefs constructed from “complex” blocks than on reefs constructed from “simple” blocks, which had a smaller surface area. Productivity rates were highest on external areas of reefs. Productivity rates decreased by 1.56%, per cm distance into the reef on complex reefs and 2.93% per cm into the reef on simple block reefs. The differences in productivity rates between reefs constructed from simple and complex blocks are assumed to reflect different current regimes and food supply between the external and internal reef areas, according to reef type. Synthesis and applications. Our results show that artificial reef design can affect secondary productivity at low trophic levels. We demonstrate that the incorporation of voids into reef blocks can lead to a greater proportion of the structure serving as functional habitat for benthic species. By including such modifications into the design of artificial reefs, it may be possible to increase the overall productivity capacity of artificial structures. Artificial reef design can affect secondary productivity of organism low trophic levels. We demonstrate that the incorporation of voids into reef blocks can lead to a greater proportion of the structure serving as functional habitat for benthic species, and a higher overall productive output for the reef.

Human‐induced climate change and ocean acidification (CC‐OA) is changing the physical and biological processes occurring within the marine environment, with poorly understood implications for marine life. Within the aquaculture sector, molluskan culture is a relatively benign method of producing a high‐quality, healthy, and sustainable protein source for the expanding human population. We modeled the vulnerability of global bivalve mariculture to impacts of CC‐OA over the period 2020–2100, under RCP8.5. Vulnerability, assessed at the national level, was dependent on CC‐OA‐related exposure, taxon‐specific sensitivity and adaptive capacity in the sector. Exposure risk increased over time from 2020 to 2100, with ten nations predicted to experience very high exposure to CC‐OA in at least one decade during the period 2020–2100. Predicted high sensitivity in developing countries resulted, primarily, from the cultivation of species that have a narrow habitat tolerance, while in some European nations (France, Ireland, Italy, Portugal, and Spain) high sensitivity was attributable to the relatively high economic value of the shellfish production sector. Predicted adaptive capacity was low in developing countries primarily due to governance issues, while in some developed countries (Denmark, Germany, Iceland, Netherlands, Sweden, and the United Kingdom) it was linked to limited species diversity in the sector. Developing and least developed nations (n = 15) were predicted to have the highest overall vulnerability. Across all nations, 2060 was identified as a tipping point where predicted CC‐OA will be associated with the greatest challenge to shellfish production. However, rapid declines in mollusk production are predicted to occur in the next decade for some nations, notably North Korea. Shellfish culture offers human society a low‐impact source of sustainable protein. This research highlights, on a global scale, the likely extent and nature of the CC‐OA‐related threat to shellfish culture and this sector enabling early‐stage adaption and mitigation. Bivalve culture has enormous potential to deliver protein for an expanding population, but bivalves are vulnerable to climate change and ocean acidification (CC‐OA). We modeled the future (2020–2100) vulnerability of global bivalve culture to CC‐OA and conclude that the greatest challenge will occur from 2060 onwards. In Asia, the threat from decreased primary productivity will be challenging to address and we recommend mitigation through diversification in the European sector.

Aquaculture is growing rapidly in response to an increasing demand for protein and the over-exploitation of wild fisheries. Mussel (family Mytilidae) production has doubled over the last decade and currently stands at 1.5 million tones production per annum. Mussels produce organic biodeposits which are dispersed around the production site and, potentially, impact the receiving environment in a number of inter-linked ways. The reported benthic impacts that occur, primarily through the accumulation of these biodeposits and associated organic enrichment, vary widely between studies. The objectives of this research were to determine the nature of the relationship between sediment redox (a proxy for oxygenation) and farm-proximity and covariables whilst accounting for, and quantifying, differences in redox between sites. Sediment cores (N = 159) were taken remotely around a random sample of mussel farms, redox was measured at 10 mm sediment depth and linked to farm-distance and sediment organic/shell content and particle size, using an additive, mixed, weighted regression model. Redox varied considerably between sites and there was a highly significant reduction (50 mV) in redox adjacent to the mussel lines. Redox increased non-linearly with distance, rising rapidly at >7 m from the farm edge. The modest reduction in sediment oxygenation in close proximity to mussel farms reported here suggests that farms located over sediments characterised by pre-existing oxygen stress are likely to exacerbate benthic species impoverishment associated with reducing sedimentary conditions whilst those located over highly oxygenated sediments are likely to increase benthic productivity.

The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the 'ecosystem approach' (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP.

Anaphylaxis is a type I hypersensitivity reaction that is potentially fatal if not promptly treated. It is a clinical diagnosis, although measurement of serial serum total mast cell tryptase (MCT) is gold standard and may help differentiate anaphylaxis from its mimics. The performance characteristics of MCT assays in anaphylaxis has been variable in previous studies, due to multiple factors including differences in the definition of anaphylaxis, methods of MCT interpretation, clinical setting of anaphylaxis, causative agents, and timing of blood sample. An international consensus equation for MCT to interpret mast cell activation has been proposed and recently validated in the context of peri-operative anaphylaxis during general anesthesia. There has been an interest in the detection of newer biomarkers in anaphylaxis including platelet activation factor (PAF), chymase, carboxypeptidase A3, dipeptidyl peptidase I (DPPI), basogranulin, and CCL-2. The key determinants of an ideal biomarker in anaphylaxis are half-life, sample handling and processing requirements, and cost. There may be a role for metabolomics and systems biology in the exploration of novel biomarkers in anaphylaxis. Future studies applying these approaches might provide greater insight into factors determining severity, clinical risk stratification, identification of mast cell disorders and improving our understanding of this relatively complex acute immunological condition. Post mortem MCT evaluation is used in Forensic Medicine during autopsy for cases involving sudden death or suspected anaphylaxis. Interpretation of post mortem MCT is challenging since there is limited published evidence and the test is confounded by multiple variables largely linked to putrefaction and site of sampling. Thus, there is no international consensus on a reference range. In this state of the art review, we will focus on the practical challenges in the laboratory diagnosis of anaphylaxis and critically appraise (a) performance characteristics of MCT in anaphylaxis in different clinical scenarios (b) the role for novel biomarkers and (c) post mortem MCT and its role in fatal anaphylaxis.

The accuracy of radio-based positioning systems will be limited by multipath interference in realistic application scenarios. This paper derives closed-form expressions for the Cramér–Rao lower bound (CRLB) on the achievable time-of-arrival (ToA) and angle-of-arrival (AoA) estimation-error variances, considering the presence of multipath radio channels, and extends these results to position estimation. The derivations are based on channel models comprising deterministic, specular multipath components as well as stochastic, diffuse/dense multipath. The derived CRLBs thus allow an evaluation of the influence of channel parameters, the geometric configuration of the environment, and system parameters such as signal bandwidth and array geometry. Our results quantify how the ToA and AoA accuracies decrease when the signal bandwidth is reduced, because more multipath will then interfere with the useful LoS component. Antenna arrays can (partly) compensate this performance loss, exploiting diversity among the multipath interference. For example, the AoA accuracy with a 16-element linear array at 1 MHz bandwidth is similar to a two-element array at 1 GHz , in the magnitude order of one degree. The ToA accuracy, on the other hand, still scales by a factor of 100 from the cm-regime to the m-regime because of the dominating influence of the signal bandwidth. The position error bound shows the relationship between the range and angle information under realistic indoor channel conditions and their different scaling behaviors as a function of the anchor–agent placement. Specular multipath components have a maximum detrimental influence near the walls. It is shown for an L-shaped room that a fairly even distribution of the position error bound can be achieved throughout the environment, using two anchors equipped with 2 × 2 -array antennas. The accuracy limit due to multipath increases from the 1–10-cm-range at 1 GHz bandwidth to the 0.5–1-m-range at 100 MHz .

Accurate biomass estimates are key to understanding a wide variety of ecological functions. In marine systems, epibenthic biomass estimates have traditionally relied on either destructive/extractive methods that are limited to horizontal soft‐sediment environments, or simplistic geometry‐based biomass conversions that are unsuitable for more complex morphologies. Consequently, there is a requirement for non‐destructive, higher‐accuracy methods that can be used in an array of environments, targeting more morphologically diverse taxa, and at ecological relevant scales. We used a combination of 3D photogrammetry, convolutional neural network (CNN) automated taxonomic identification, and taxa‐specific biovolume:biomass calibrations to test the viability of estimating biomass of three species of morphologically complex epibenthic taxa from in situ stereo 2D source imagery. Our trained CNN produced accurate and reliable annotations of our target taxa across a wide range of conditions. When incorporated into photogrammetric 3D models of underwater surveys, we were able to automatically isolate our three target taxa from their environment, producing biovolume measurements that had respective mean similarities of 99%, 102% and 120% of those obtained from human annotators. When combined with taxa‐specific biovolume:biomass calibration values, we produced biomass estimates of 88%, 125% and 133% mean similarity to that of the ‘true’ biomass of the respective taxa. Our methodology provides a highly reliable and efficient method for estimating epibenthic biomass of morphologically complex taxa using non‐destructive 2D imagery. This approach can be applied to a variety of environments and photo/video survey approaches (e.g. SCUBA, ROV, AUV) and is especially valuable in spatially extensive surveys where manual approaches are prohibitively time‐consuming.