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The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776)
No full textWe present a genome assembly from an individual Clavelina lepadiformis (the light-bulb sea squirt; Chordata; Ascidiacea; Aplousobranchia; Clavelinidae). The genome sequence is 210.1 megabases in span. Most of the assembly is scaffolded into 9 chromosoma
Global tracking of shark movements, behaviour and ecology: A review of the renaissance years of satellite tagging studies, 2010–2020
No full textSatellite telemetry as a tool in marine ecological research continues to adapt and grow and has become increasingly popular in recent years to study shark species on a global scale. A review of satellite tag application to shark research was published in 2010, provided insight to the advancements in satellite shark tagging, as well as highlighting areas for improvement. In the years since, satellite technology has continued to advance, creating smaller, longer lasting, and more innovative tags, capable of expanding the field. Here we review satellite shark tagging studies to identify early successes and areas for rethinking moving forward. Triple the amount of shark satellite tagging studies have been conducted during the decade from 2010 to 2020 than ever before, tracking double the number of species previously tagged. Satellite telemetry has offered increased capacity to unravel ecological questions including predator and prey interactions, migration patterns, habitat use, in addition to monitoring species for global assessments. However, <17% of the total reviewed studies directly produced results with management or conservation outcomes. Telemetry studies with defined goals and objectives produced the most relevant findings for shark conservation, most often in tandem with secondary metrics such as fishing overlap or management regimes. To leverage the power of telemetry for the benefit of shark species, it remains imperative to continue improvements to tag function and maximize the outputs of tagging efforts including increasing data sharing capacity and standardization across the field, as well as spatial and species coverage. Ultimately, this review offers a status report of shark satellite tagging and the ways in which the field can continue to progress
Seeps and vents of the Bering Sea
Get PDFThis special issue focuses on hydrothermal vent and methane seep fauna and communities in the Bering Sea. Although fragmentary information has been previously published on the hydrothermal vents, data on methane seep communities from the Bering Sea are presented here for the first time.
Hydrocarbon seeps and hydrothermal vents provide specific habitats that are influenced by seabed emissions of fluids rich in reduced compounds. Communities inhabiting hydrothermal vents and seeps below the photic zone, mostly depend on autochthonous primary organic matter synthesized by symbiotic and free-living microbes through chemoautolithotrophy or methanotrophy. Chemosynthetic communities are highly productive, compared to the surrounding benthic areas.
Discovered nearly 40 years ago (Corliss et al., 1979; Paull et al., 1984), and intensively studied since then (Van Dover, 2000; German et al., 2011; Levin et al., 2016 and others), vent and seep communities are still of great research interest. This includes: faunistic and ecological distinctiveness of chemosynthetic communities, adaptations to extreme conditions and understanding the evolution of marine ecosystems. Recent proposals for seabed mineral exploitation also require knowledge on chemosynthetic ecosystems for rational management decisions (Jones et al., 2020; Van Dover et al., 2018)
Planning precision aquaculture activities in a changing and crowded sea
Get PDFExtreme climate events are increasingly challenging the growth of the marine aquaculture sector, causing local influences on species performance and affecting production and yield - impacting where to locate cage aquaculture facilities. Here we produced scenario-based quantitative maps using modelled species-specific performance combined with predicted high-resolution future IPCC temperature scenarios. We ran a species-specific Dynamic Energy Budget mechanistic model for four model species, up to 2050, and mapped functional trait-based outcomes as: i) time to reach the commercial size, ii) feces produced and iii) uneaten food. A high spatial resolution suitability index allowed the sustainability of farming strategies for single- and multi-species to be identified across a 159.696 km2 surface extension (Italian Exclusive Economic Zone; 6% of the Mediterranean basin surface). Providing a good case study to shed light on difficult questions facing aquaculture planning around the world. Good future performance under both representative concentration pathway (RCP) scenarios were modelled for Sea bream and European seabass in inshore waters. Performance of Mediterranean mussels and Japanese oysters was found to decrease slightly when compared to the 2007–2010 time interval. Scenario-based quantitative maps represent a heterogeneous species-specific knowledge layer that is critical to better inform aquaculture management and development strategies. Yet this knowledge layer is missing from the process to develop climate-resilient risk maps and associated adaptation measures, as well as when informing stakeholders on potential site expansion and/or the establishment of nascent aquaculture industry sites
To what extent can decommissioning options for marine artificial structures move us toward environmental targets?
Get PDFSwitching from fossil fuels to renewable energy is key to international energy transition efforts and the move
toward net zero. For many nations, this requires decommissioning of hundreds of oil and gas infrastructure in the marine environment. Current international, regional and national legislation largely dictates that structures must
be completely removed at end-of-life although, increasingly, alternative decommissioning options are being
promoted and implemented. Yet, a paucity of real-world case studies describing the impacts of decommissioning
on the environment make decision-making with respect to which option(s) might be optimal for meeting in�ternational and regional strategic environmental targets challenging. To address this gap, we draw together
international expertise and judgment from marine environmental scientists on marine artificial structures as an
alternative source of evidence that explores how different decommissioning options might ameliorate pressures
that drive environmental status toward (or away) from environmental objectives. Synthesis reveals that for 37
United Nations and Oslo-Paris Commissions (OSPAR) global and regional environmental targets, experts consider
repurposing or abandoning individual structures, or abandoning multiple structures across a region, as the op�tions that would most strongly contribute toward targets. This collective view suggests complete removal may
not be best for the environment or society. However, different decommissioning options act in different ways and
make variable contributions toward environmental targets, such that policy makers and managers would likely
need to prioritise some targets over others considering political, social, economic, and ecological contexts.
Current policy may not result in optimal outcomes for the environment or society
Inhalable Textile Microplastic Fibers Impair Airway Epithelial Differentiation
Get PDFRationale: Microplastics are a pressing global concern and inhalation of microplastic fibers has been associated with interstitial and bronchial inflammation in flock workers. However, how microplastic fibers affect the lungs is unknown. Objectives: Our aim was to assess the effects of 12x31 µm nylon 6,6 (nylon) and 15x52 µm polyethylene terephthalate (polyester) textile microplastic fibers on lung epithelial growth and differentiation. Methods: We used human and murine alveolar and airway-type organoids as well as air-liquid interface cultures derived from primary lung epithelial progenitor cells and incubated these with either nylon or polyester fibers or nylon leachate. In addition, mice received one dose of nylon fibers or nylon leachate and 7 days later organoid-forming capacity of isolated epithelial cells was investigated. Measurements and Main Results: We observed that nylon microfibers, more than polyester, inhibited developing airway organoids and not established ones. This effect was mediated by components leaching from nylon. Epithelial cells isolated from mice exposed to nylon fibers or leachate, also formed fewer airway organoids, suggesting long-lasting effects of nylon components on epithelial cells. Part of these effects were recapitulated in human air-liquid interface cultures. Transcriptome analysis revealed upregulation of Hoxa5 post-exposure to nylon fibers. Inhibiting Hoxa5 during nylon exposure restored airway organoid formation, confirming Hoxa5's pivotal role in the effects of nylon. Conclusions: These results suggest that components leaching from nylon 6,6 may especially harm developing airways and/or airways undergoing repair and we strongly encourage to characterize both hazard of and exposure to microplastic fibers in more detail
TLS2trees: A scalable tree segmentation pipeline for TLS data
Get PDF1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In
recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done
manually (e.g. with interactive point cloud editing software) and can be very time consuming.
2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2treesconsists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data cap�tured across 10 plots of seven forest types; from open savanna to dense tropical rainforest.
3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3
and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of se�mantic segmentation step.
4. The volume and scale of TLS data captured in forest plots is increasing. It is sug�gested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser
scanning), TLS2trees is a free and open-source software
Mesoscale oceanographic meanders influence protist community function and structure in the southern Indian Ocean
Get PDFThe interface between the nutrient-rich Southern Ocean and oligotrophic Indian Ocean creates unique environmental conditions that can strongly influence biological processes. We investigated protist communities across a mesoscale meander of the Subtropical Front within the Southern Indian Ocean. 18S V9 rDNA metabarcoding suggests a diverse protist community in which the dinoflagellates and parasitic Syndiniales were abundant. Diversity was highest in frontal waters of the mesoscale meander, with differences in community structure inside and outside the meander. While the overall community was dominated by mixotrophic taxa, the frontal boundary of the meander had increased abundances of heterotrophic taxa, with potential implications for net atmospheric CO2 drawdown. Pulse amplitude modulated (PAM) fluorimetry revealed significant differences in the photophysiology of phytoplankton communities inside and outside the meander. By using single-cell PAM microscopy, we identified physiological differences between dinoflagellate and coccolithophore taxa, which may have contributed to changes in photophysiology observed at community level. Overall, our results demonstrate that frontal areas have a strong impact on the composition of protist communities in the Southern Ocean with important implications for understanding biological processes in this region
Characterization of the molecular mechanisms of silicon uptake in coccolithophores
Get PDFCoccolithophores are an important group of calcifying marine phytoplankton. Although coccolithophores are not silicified, some species exhibit a requirement for Si in the calcification process. These species also possess a novel protein (SITL) that resembles the SIT family of Si transporters found in diatoms. However, the nature of Si transport in coccolithophores is not yet known, making it difficult to determine the wider role of Si in coccolithophore biology. Here, we show that coccolithophore SITLs act as Na+-coupled Si transporters when expressed in heterologous systems and exhibit similar characteristics to diatom SITs. We find that CbSITL from Coccolithus braarudii is transcriptionally regulated by Si availability and is expressed in environmental coccolithophore populations. However, the Si requirement of C. braarudii and other coccolithophores is very low, with transport rates of exogenous Si below the level of detection in sensitive assays of Si transport. As coccoliths contain only low levels of Si, we propose that Si acts to support the calcification process, rather than forming a structural component of the coccolith itself. Si is therefore acting as a micronutrient in coccolithophores and natural populations are only likely to experience Si limitation in circumstances where dissolved silicon (DSi) is depleted to extreme levels
Improving the performance of National Centre for Earth Observation (NCEO) code using GPUs
Get PDFThe aim of this study was to investigate the advantages of different tools designed for running code on Graphics Processing Units (GPUs) and specify the types of code best suited for GPU acceleration.
• Three examples of code were obtained from NCEO scientists for three distinct applications and ported to GPUs on the Natural Environment Research Council (NERC) Earth Observation Data Acquisition and Analysis Service (NEODAAS) MAGEO computing cluster.
• Comparisons were made between the time taken to run the code on the original Central Processing Unit (CPU) and the MAGEO CPU and GPU.
• Accelerations of between x30 and x1800 were achieved: more details are provided below.
• In terms of energy saving this relates to an estimated 93.9% to 99.8% reduction in electricity usage.
• The study highlighted the value of expertise in GPUs and coding such as provided by NEODAA