Combining acoustic telemetry with archival tagging to investigate the spatial dynamic of the understudied pollack, Pollachius pollachius.

Combining fish tracking methods is a promising way of leveraging the strengths of each approach while mitigating their individual weaknesses. Acoustic telemetry provides presence information as the fish move within receiver range, eliminating the need for tag recovery. Archival tags, on the other hand, record environmental variables on tag retrieval, enabling continuous path reconstruction of a fish beyond coastal regions. This study capitalizes on the combination of both methods for geolocating pollack, Pollachius pollachius, an understudied species of the northeast Atlantic, where declining stocks are raising concern. Essential knowledge of population structure and connectivity between essential habitats is critically lacking and could help inform stock assessment and management. The aims of the study were (1) to evaluate the feasibility of double-tagging pollack, known for being challenging to tag, and (2) to track seasonal movements across the Channel to gain first insights into pollack spatial ecology. In 2022, an extensive network of acoustic receivers was been deployed in the Channel along the French, English, and Belgian coasts as part of the Fish Intel project. We tagged 83 pollack with acoustic transmitters, among which 48 were double-tagged with data storage tags. Post-tagging survival assessment, conducted on a subset of 35 individuals, revealed a successful procedure with a 97% short-term survival rate. By October 2023, the acoustic telemetry network detected 30 out of 83 pollack at least once, with no large-scale movements observed across the Channel. Presence in the network fluctuates seasonally, peaking in summer, particularly among immature fish. Integrating acoustic detections with temperature and depth time series in a geolocation model enabled trajectory reconstruction of 10 recaptured pollack, seven of which were detected by the network. This combined tracking approach revealed coastal movements along the coast of Brittany in France, highlighting the ecological significance of the Iroise Sea for pollack throughout the year, particularly in summer. The geolocation model also suggested movements towards the entrance of the western Channel. This study highlights the complementarity of acoustic telemetry and archival tagging in reconstructing fish movements in their natural environment. As data accumulate, these innovative tracking methods promise to continually unveil new insights into the spatial ecology of the understudied pollack, which is essential for the species' management.

Respiratory mucosal immune memory to SARS-CoV-2 after infection and vaccination.

Respiratory mucosal immunity induced by vaccination is vital for protection from coronavirus infection in animal models. In humans, the capacity of peripheral vaccination to generate sustained immunity in the lung mucosa, and how this is influenced by prior SARS-CoV-2 infection, is unknown. Here we show using bronchoalveolar lavage samples that donors with history of both infection and vaccination have more airway mucosal SARS-CoV-2 antibodies and memory B cells than those only vaccinated. Infection also induces populations of airway spike-specific memory CD4+ and CD8+ T cells that are not expanded by vaccination alone. Airway mucosal T cells induced by infection have a distinct hierarchy of antigen specificity compared to the periphery. Spike-specific T cells persist in the lung mucosa for 7 months after the last immunising event. Thus, peripheral vaccination alone does not appear to induce durable lung mucosal immunity against SARS-CoV-2, supporting an argument for the need for vaccines targeting the airways.

Detecting sediment recovery below an offshore longline mussel farm: A macrobenthic Biological Trait Analysis (BTA).

Expansion of bivalve aquaculture offshore reports lower environmental impacts compared to inshore farms. Taking a Before-After Control-Impact approach, this study presents the first functional diversity analysis and long-term Biological Trait Analysis (BTA) of infauna functional traits following the development of the United Kingdom's first large-scale, offshore longline mussel farm. Located in an area historically impacted by mobile fishing gear, farm sites had the greatest number of taxa and abundance compared to control sites. Functional diversity varied significantly across treatments (farm, near control, far control); while Functional Diversity, Richness, Divergence and Dispersion increased over time within the farm, Functional Evenness and Redundancy decreased. Bioturbation, body size, diet, feeding mode, life span, motility, sediment position, sensitivity and substrate type were chosen for Community-level Weighted Mean analysis, depicting the most frequently affected biological traits by shellfish farming. Farm sites developed a wider range of traits enhancing ecosystem function and habitat recovery after years of seabed damage. Outcomes support the use of functional diversity and BTA analysis to perform ecosystem assessment, supporting decision-makers implement policy and management.

A novel method for identifying coded tags recorded on aquatic acoustic monitoring systems.

Aquatic biotelemetry increasingly relies on using acoustic transmitters ('tags') that enable passive detection of tagged animals using fixed or mobile receivers. Both tracking methods are resource-limited, restricting the spatial area in which movements of highly mobile animals can be measured using proprietary detection systems. Transmissions from tags are recorded by underwater noise monitoring systems designed for other purposes, such as cetacean monitoring devices, which have been widely deployed in the marine environment; however, no tools currently exist to decode these detections, and thus valuable additional information on animal movements may be missed. Here, we describe simple hybrid methods, with potentially wide application, for obtaining information from otherwise unused data sources. The methods were developed using data from moored, acoustic cetacean detectors (C-PODs) and towed passive receiver arrays, often deployed to monitor the vocalisations of cetaceans, but any similarly formatted data source could be used. The method was applied to decode tag detections that were found to have come from two highly mobile fish species, bass (Dicentrarchus labrax) and Twaite shad (Alosa fallax), that had been tagged in other studies. Decoding results were validated using test tags; range testing data were used to demonstrate the relative efficiency of these receiver methods in detecting tags. This approach broadens the range of equipment from which acoustic tag detections can be decoded. Novel detections derived from the method could add significant value to past and present tracking studies at little additional cost, by providing new insights into the movement of mobile animals at sea.

LI-Detector: a Method for Curating Ordered Gene-Replacement Libraries.

In recent years the availability of genome sequence information has grown logarithmically resulting in the identification of a plethora of uncharacterized genes. To address this gap in functional annotation, many high-throughput screens have been devised to uncover novel gene functions. Gene-replacement libraries are one such tool that can be screened in a high-throughput way to link genotype and phenotype and are key community resources. However, for a phenotype to be attributed to a specific gene, there needs to be confidence in the genotype. Construction of large libraries can be laborious and occasionally errors will arise. Here, we present a rapid and accurate method for the validation of any ordered library where a gene has been replaced or disrupted by a uniform linear insertion (LI). We applied our method (LI-detector) to the well-known Keio library of Escherichia coli gene-deletion mutants. Our method identified 3,718 constructed mutants out of a total of 3,728 confirmed isolates, with a success rate of 99.7% for identifying the correct kanamycin cassette position. This data set provides a benchmark for the purity of the Keio mutants and a screening method for mapping the position of any linear insertion, such as an antibiotic resistance cassette in any ordered library. IMPORTANCE The construction of ordered gene replacement libraries requires significant investment of time and resources to create a valuable community resource. During construction, technical errors may result in a limited number of incorrect mutants being made. Such mutants may confound the output of subsequent experiments. Here, using the remarkable E. coli Keio knockout library, we describe a method to rapidly validate the construction of every mutant.

Reactogenicity and immunogenicity after a late second dose or a third dose of ChAdOx1 nCoV-19 in the UK: a substudy of two randomised controlled trials (COV001 and COV002).

BACKGROUND: COVID-19 vaccine supply shortages are causing concerns about compromised immunity in some countries as the interval between the first and second dose becomes longer. Conversely, countries with no supply constraints are considering administering a third dose. We assessed the persistence of immunogenicity after a single dose of ChAdOx1 nCoV-19 (AZD1222), immunity after an extended interval (44-45 weeks) between the first and second dose, and response to a third dose as a booster given 28-38 weeks after the second dose. METHODS: In this substudy, volunteers aged 18-55 years who were enrolled in the phase 1/2 (COV001) controlled trial in the UK and had received either a single dose or two doses of 5 × 1010 viral particles were invited back for vaccination. Here we report the reactogenicity and immunogenicity of a delayed second dose (44-45 weeks after first dose) or a third dose of the vaccine (28-38 weeks after second dose). Data from volunteers aged 18-55 years who were enrolled in either the phase 1/2 (COV001) or phase 2/3 (COV002), single-blinded, randomised controlled trials of ChAdOx1 nCoV-19 and who had previously received a single dose or two doses of 5 × 1010 viral particles are used for comparison purposes. COV001 is registered with ClinicalTrials.gov, NCT04324606, and ISRCTN, 15281137, and COV002 is registered with ClinicalTrials.gov, NCT04400838, and ISRCTN, 15281137, and both are continuing but not recruiting. FINDINGS: Between March 11 and 21, 2021, 90 participants were enrolled in the third-dose boost substudy, of whom 80 (89%) were assessable for reactogenicity, 75 (83%) were assessable for evaluation of antibodies, and 15 (17%) were assessable for T-cells responses. The two-dose cohort comprised 321 participants who had reactogenicity data (with prime-boost interval of 8-12 weeks: 267 [83%] of 321; 15-25 weeks: 24 [7%]; or 44-45 weeks: 30 [9%]) and 261 who had immunogenicity data (interval of 8-12 weeks: 115 [44%] of 261; 15-25 weeks: 116 [44%]; and 44-45 weeks: 30 [11%]). 480 participants from the single-dose cohort were assessable for immunogenicity up to 44-45 weeks after vaccination. Antibody titres after a single dose measured approximately 320 days after vaccination remained higher than the titres measured at baseline (geometric mean titre of 66·00 ELISA units [EUs; 95% CI 47·83-91·08] vs 1·75 EUs [1·60-1·93]). 32 participants received a late second dose of vaccine 44-45 weeks after the first dose, of whom 30 were included in immunogenicity and reactogenicity analyses. Antibody titres were higher 28 days after vaccination in those with a longer interval between first and second dose than for those with a short interval (median total IgG titre: 923 EUs [IQR 525-1764] with an 8-12 week interval; 1860 EUs [917-4934] with a 15-25 week interval; and 3738 EUs [1824-6625] with a 44-45 week interval). Among participants who received a third dose of vaccine, antibody titres (measured in 73 [81%] participants for whom samples were available) were significantly higher 28 days after a third dose (median total IgG titre: 3746 EUs [IQR 2047-6420]) than 28 days after a second dose (median 1792 EUs [IQR 899-4634]; Wilcoxon signed rank test p=0·0043). T-cell responses were also boosted after a third dose (median response increased from 200 spot forming units [SFUs] per million peripheral blood mononuclear cells [PBMCs; IQR 127-389] immediately before the third dose to 399 SFUs per milion PBMCs [314-662] by day 28 after the third dose; Wilcoxon signed rank test p=0·012). Reactogenicity after a late second dose or a third dose was lower than reactogenicity after a first dose. INTERPRETATION: An extended interval before the second dose of ChAdOx1 nCoV-19 leads to increased antibody titres. A third dose of ChAdOx1 nCoV-19 induces antibodies to a level that correlates with high efficacy after second dose and boosts T-cell responses. FUNDING: UK Research and Innovation, Engineering and Physical Sciences Research Council, National Institute for Health Research, Coalition for Epidemic Preparedness Innovations, National Institute for Health Research Oxford Biomedical Research Centre, Chinese Academy of Medical Sciences Innovation Fund for Medical Science, Thames Valley and South Midlands NIHR Clinical Research Network, AstraZeneca, and Wellcome.

Optimal fishing effort benefits fisheries and conservation.

The ecosystem effects of all commercial fishing methods need to be fully understood in order to manage our marine environments more effectively. The impacts associated with the most damaging mobile fishing methods are well documented leading to such methods being removed from some partially protected areas. In contrast, the impacts on the ecosystem from static fishing methods, such as pot fishing, are less well understood. Despite commercial pot fishing increasing within the UK, there are very few long term studies (> 1 year) that consider the effects of commercial pot fishing on temperate marine ecosystems. Here we present the results from a controlled field experiment where areas of temperate reef were exposed to a pot fishing density gradient over 4 years within a Marine Protected Area (MPA), simulating scenarios both above and below current levels of pot fishing effort. After 4 years we demonstrate for the first time negative effects associated with high levels of pot fishing effort both on reef building epibiota and commercially targeted species, contrary to existing evidence. Based on this new evidence we quantify a threshold for sustainable pot fishing demonstrating a significant step towards developing well-managed pot fisheries within partially protected temperate MPAs.

The impact of potting for crustaceans on temperate rocky reef habitats: Implications for management.

Multi-use marine protected areas (MPAs) are increasingly designated towards achieving global conservation targets. To develop effective management, the impact of permitted activities must be understood. Potting for shellfish occurs on temperate rocky reefs globally with impact not fully quantified. This UK-based study used underwater video to quantify (a) benthic condition of rocky reefs, (b) mechanisms of potting interaction and (c) true footprint of potting. Assemblages in static gear areas were more indicative of a healthy reef than those in mixed gear areas. Damage was recorded during pot hauling, but the area of damage was not the entire pot haul path. 25-30% of individuals were damaged (commonly through tissue abrasion) or removed. Notably, damage occurred to some long-lived, slow growing taxa raising concerns over impacts. Potting is more destructive than previously thought and managers must balance ecology with social and economic considerations to determine what level of impact is acceptable.

PelagiCam: a novel underwater imaging system with computer vision for semi-automated monitoring of mobile marine fauna at offshore structures.

Engineered structures in the open ocean are becoming more frequent with the expansion of the marine renewable energy industry and offshore marine aquaculture. Floating engineered structures function as artificial patch reefs providing novel and relatively stable habitat structure not otherwise available in the pelagic water column. The enhanced physical structure can increase local biodiversity and benefit fisheries yet can also facilitate the spread of invasive species. Clear evidence of any ecological consequences will inform the design and placement of structures to either minimise negative impacts or enhance ecosystem restoration. The development of rapid, cost-effective and reliable remote underwater monitoring methods is crucial to supporting evidence-based decision-making by planning authorities and developers when assessing environmental risks and benefits of offshore structures. A novel, un-baited midwater video system, PelagiCam, with motion-detection software (MotionMeerkat) for semi-automated monitoring of mobile marine fauna, was developed and tested on the UK's largest offshore rope-cultured mussel farm in Lyme Bay, southwest England. PelagiCam recorded Atlantic horse mackerel (Trachurus trachurus), garfish (Belone belone) and two species of jellyfish (Chrysaora hysoscella and Rhizostoma pulmo) in open water close to the floating farm structure. The software successfully distinguished video frames where fishes were present versus absent. The PelagiCam system provides a cost-effective remote monitoring tool to streamline biological data acquisition in impact assessments of offshore floating structures. With the rise of sophisticated artificial intelligence for object recognition, the integration of computer vision techniques should receive more attention in marine ecology and has great potential to revolutionise marine biological monitoring.

A simple mooring modification reduces impacts on seagrass meadows.

Moorings can have a detrimental impact on seagrass, fragmenting the meadows, resulting in the habitat degradation. To reduce contact of the moorings with the seabed we attached small floats along the chain of a traditional swing mooring and monitored the ecological impacts of this modified mooring, with reference to a standard swing mooring, in a seagrass meadow under high tidal influence. After three years, seagrass density surrounding the modified mooring was over twice as high as that of the standard mooring, with blade length surrounding the modified mooring also found to exceed that of the standard mooring. Seagrass-associated epifaunal species richness was twice as high surrounding the modified mooring compared to the standard mooring. Sediment composition was considerably finer at the modified mooring, indicative of increased disturbance surrounding the standard mooring. A simple modification to existing swing moorings can mitigate some of the impacts of moorings on seagrass meadows, whilst accommodating for tidal fluctuations. The scale of the differences observed between the mooring types demonstrates the susceptibility of seagrass meadows to damage from swing moorings. Given the ecological importance of these habitats, it is crucial that action is taken to reduce further degradation, such as that demonstrated here.

Motion in the ocean-Paradigm shift in movement ecology requires "sedentary" organisms to be redefined.

In Focus: Hamel, J.-F., Sun, J., Gianasi, B. L., et al. (2019). Active buoyancy adjustment increases dispersal potential in benthic marine animals. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.12943 Effective ecosystem-based fisheries and conservation management relies on the accuracy of population structure and connectivity models. The majority of sedentary marine species are pelago-benthic, meaning the pelagic larval stages disperse using ocean currents, and the adults are stationary or crawl slowly over the seabed. Adult movement was, until recently, thought to be insignificant due to the limited spatial range. In this issue, a novel method of translocation for adults that may far exceed the dispersion capability of the juveniles is presented, providing evidence for important effects of adult dispersal. Active buoyancy adjustment (ABA) is a behavioural response to environmental stressors or water currents that enables echinoderm Asteroidea (sea stars) and Holothuroidea (sea cucumbers) to efficiently relocate. Adult relocation using tides could explain mass spawning aggregations that increase population and individual fitness, and less advantageous mass stranding events. Implications of ABA for future marine management and policy are discussed.

Assessing the impact of introduced infrastructure at sea with cameras: A case study for spatial scale, time and statistical power.

Detecting the effects of introduced artificial structures on the marine environment relies upon research and monitoring programs that can provide baseline data and the necessary statistical power to detect biological and/or ecological change over relevant spatial and temporal scales. Here we report on, and assess the use of, Baited Remote Underwater Video (BRUV) systems as a technique to monitor diversity, abundance and assemblage composition data to evaluate the effects of marine renewable energy infrastructure on mobile epi-benthic species. The results from our five-year study at a wave energy development facility demonstrate how annual natural variation (time) and survey design (spatial scale and power) are important factors in the ability to robustly detect change in common ecological metrics of benthic and bentho-pelagic ecosystems of the northeast Atlantic. BRUV systems demonstrate their capacity for use in temperate, high energy marine environments, but also how weather, logistical and technical issues require increased sampling effort to ensure statistical power to detect relevant change is achieved. These factors require consideration within environmental impact assessments if such survey methods are to identify and contribute towards the management of potential positive or negative effects on benthic systems.

Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants.

Members of the eukaryotic translation initiation factor (eIF) gene family, including eIF4E and its paralogue eIF(iso)4E, have previously been identified as recessive resistance alleles against various potyviruses in a range of different hosts. However, the identification and introgression of these alleles into important crop species is often limited. In this study, we utilise CRISPR/Cas9 technology to introduce sequence-specific deleterious point mutations at the eIF(iso)4E locus in Arabidopsis thaliana to successfully engineer complete resistance to Turnip mosaic virus (TuMV), a major pathogen in field-grown vegetable crops. By segregating the induced mutation from the CRISPR/Cas9 transgene, we outline a framework for the production of heritable, homozygous mutations in the transgene-free T2 generation in self-pollinating species. Analysis of dry weights and flowering times for four independent T3 lines revealed no differences from wild-type plants under standard growth conditions, suggesting that homozygous mutations in eIF(iso)4E do not affect plant vigour. Thus, the established CRISPR/Cas9 technology provides a new approach for the generation of Potyvirus resistance alleles in important crops without the use of persistent transgenes.

A legal and ecological perspective of 'site integrity' to inform policy development and management of Special Areas of Conservation in Europe.

The European Union Habitats Directive (92/43/EEC) provides for the designation and management of Special Areas of Conservation (SACs) and requires that impacting activities are subject to 'an appropriate assessment' of their implications for the 'integrity' of the site. We define the term 'site integrity' from a legal and an ecological perspective. We demonstrate that 'site integrity' is the maintenance of ecological processes and functions that support the wider delivery of ecosystem services. 'Site integrity' can be influenced by SAC management. Management that seeks to support 'site integrity' may include the use of buffer zones or connecting areas that extend beyond the SAC site's designated features. We conclude that 'site integrity' and 'favourable conservation status' are powerful legal terms that if fully transposed into the law and policy of Member States can enable the achievement of broader European and International goals for marine conservation.

Epibenthic assessment of a renewable tidal energy site.

Concern over global climate change as a result of fossil fuel use has resulted in energy production from renewable sources. Marine renewable energy devices provide clean electricity but can also cause physical disturbance to the local environment. There is a considerable paucity of ecological data at potential marine renewable energy sites that is needed to assess potential future impacts and allow optimal siting of devices. Here, we provide a baseline benthic survey for the Big Russel in Guernsey, UK, a potential site for tidal energy development. To assess the suitability of proposed sites for marine renewable energy in the Big Russel and to identify potential control sites, we compared species assemblages and habitat types. This baseline survey can be used to select control habitats to compare and monitor the benthic communities after installation of the device and contribute towards the optimal siting of any future installation.

Recovery of a temperate reef assemblage in a marine protected area following the exclusion of towed demersal fishing.

Marine Protected Areas MPA have been widely used over the last 2 decades to address human impacts on marine habitats within an ecosystem management context. Few studies have quantified recovery of temperate rocky reef communities following the cessation of scallop dredging or demersal trawling. This is critical information for the future management of these habitats to contribute towards conservation and fisheries targets. The Lyme Bay MPA, in south west UK, has excluded towed demersal fishing gear from 206 km(2) of sensitive reef habitat using a Statutory Instrument since July 2008. To assess benthic recovery in this MPA we used a flying video array to survey macro epi-benthos annually from 2008 to 2011. 4 treatments (the New Closure, previously voluntarily Closed Controls and Near or Far Open to fishing Controls) were sampled to test a recovery hypothesis that was defined as 'the New Closure becoming more similar to the Closed Controls and less similar to the Open Controls'. Following the cessation of towed demersal fishing, within three years positive responses were observed for species richness, total abundance, assemblage composition and seven of 13 indicator taxa. Definitive evidence of recovery was noted for species richness and three of the indicator taxa (Pentapora fascialis, Phallusia mammillata and Pecten maximus). While it is hoped that MPAs, which exclude anthropogenic disturbance, will allow functional restoration of goods and services provided by benthic communities, it is an unknown for temperate reef systems. Establishing the likely timescales for restoration is key to future marine management. We demonstrate the early stages of successful recruitment and link these to the potential wider ecosystem benefits including those to commercial fisheries.

A quantitative, non-destructive methodology for habitat characterisation and benthic monitoring at offshore renewable energy developments.

Following governments' policies to tackle global climate change, the development of offshore renewable energy sites is likely to increase substantially over coming years. All such developments interact with the seabed to some degree and so a key need exists for suitable methodology to monitor the impacts of large-scale Marine Renewable Energy Installations (MREIs). Many of these will be situated on mixed or rocky substrata, where conventional methods to characterise the habitat are unsuitable. Traditional destructive sampling is also inappropriate in conservation terms, particularly as safety zones around (MREIs) could function as Marine Protected Areas, with positive benefits for biodiversity. Here we describe a technique developed to effectively monitor the impact of MREIs and report the results of its field testing, enabling large areas to be surveyed accurately and cost-effectively. The methodology is based on a high-definition video camera, plus LED lights and laser scale markers, mounted on a "flying array" that maintains itself above the seabed grounded by a length of chain, thus causing minimal damage. Samples are taken by slow-speed tows of the gear behind a boat (200 m transects). The HD video and randomly selected frame grabs are analysed to quantify species distribution. The equipment was tested over two years in Lyme Bay, UK (25 m depth), then subsequently successfully deployed in demanding conditions at the deep (>50 m) high-energy Wave Hub site off Cornwall, UK, and a potential tidal stream energy site in Guernsey, Channel Islands (1.5 ms⁻¹ current), the first time remote samples from such a habitat have been achieved. The next stage in the monitoring development process is described, involving the use of Remote Operated Vehicles to survey the seabed post-deployment of MREI devices. The complete methodology provides the first quantitative, relatively non-destructive method for monitoring mixed-substrate benthic communities beneath MPAs and MREIs pre- and post-device deployment.

Recovery of meiofauna communities following mudflat disturbance by trampling associated with crab-tiling.

The provision of artificial shelters for the collection of crabs, known as crab-tiling, and the subsequent harvesting of the soft "peeler" crabs for angling bait, are associated with trampling disturbance of intertidal mudflats in the United Kingdom. Recovery of meiofauna communities following crab-tiling activity was investigated on an intertidal mudflat in SW England. Harvesting of experimental plots was reproduced six times over a 2-week period. Meiofauna was collected at low tides 12h, 36 h and 144 h after treatment. Meiofaunal and nematode abundance, and nematode species number, was significantly greater in controls compared to crab-tile stations at 12h. At 36 h and 144 h there were no significant differences between treatments, indicating recovery had occurred in 12-36 h. Multivariate analysis showed nematode assemblage composition from control plots to be significantly different from crab-tile plots at 12h. No significant differences were observed between sediment physical parameters with treatment. Results suggest that the predominant effect of disturbance may be vibration-induced burial, which causes nematodes to bury deeper into the sediment, beyond the depth sampled, and explains the rapid recovery.