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Abstract We sampled 17 nesting sites for loggerhead (Caretta caretta) and green turtles (Chelonia mydas) in Cyprus. Microplastics (<5 mm) were found at all locations and depths, with particularly high abundance in superficial sand. The top 2 cm of sand presented grand mean ± SD particle counts of 45,497 ± 11,456 particles m−3 (range 637–131,939 particles m−3). The most polluted beaches were among the worst thus far recorded, presenting levels approaching those previously recorded in Guangdong, South China. Microplastics decreased with increasing sand depth but were present down to turtle nest depths of 60 cm (mean 5,325 ± 3,663 particles m−3. Composition varied among beaches but hard fragments (46.5 ± 3.5%) and pre-production nurdles (47.8 ± 4.5%) comprised most categorised pieces. Particle drifter analysis hindcast for 365 days indicated that most plastic likely originated from the eastern Mediterranean basin. Worsening microplastic abundance could result in anthropogenically altered life history parameters such as hatching success and sex ratios in marine turtles. Highlights • Microplastics were found at all locations and depths at 17 marine turtle nesting beaches in Cyprus. • Particularly high abundance in top 2 cm of sand but were present down to turtle nest depths of 60 cm. • Hard fragments and pre-production nurdles comprised most categorised pieces of microplastic. • Particle drifter analysis indicated plastic originated from the eastern Mediterranean basin. • High abundance could result in anthropogenic altered life history parameters in marine turtles. [ABSTRACT FROM AUTHOR]

Lagrangian analysis is a powerful way to analyse the output of ocean circulation models and other ocean velocity data such as from altimetry. In the Lagrangian approach, large sets of virtual particles are integrated within the three-dimensional, time-evolving velocity fields. Over several decades, a variety of tools and methods for this purpose have emerged. Here, we review the state of the art in the field of Lagrangian analysis of ocean velocity data, starting from a fundamental kinematic framework and with a focus on large-scale open ocean applications. Beyond the use of explicit velocity fields, we consider the influence of unresolved physics and dynamics on particle trajectories. We comprehensively list and discuss the tools currently available for tracking virtual particles. We then showcase some of the innovative applications of trajectory data, and conclude with some open questions and an outlook. The overall goal of this review paper is to reconcile some of the different techniques and methods in Lagrangian ocean analysis, while recognising the rich diversity of codes that have and continue to emerge, and the challenges of the coming age of petascale computing. [ABSTRACT FROM AUTHOR]

There are fundamental gaps in our understanding of the fates of microplastics in the ocean, which must be overcome if the severity of this pollution is to be fully assessed. The predominant pattern is high accumulation of microplastic in subtropical gyres. Using in situ measurements from the 7th Continent expedition in the North Atlantic subtropical gyre, data from satellite observations and models, we show how microplastic concentrations were up to 9.4 times higher in an anticyclonic eddy explored, compared to the cyclonic eddy. Although our sample size is small, this is the first suggestive evidence that mesoscale eddies might trap, concentrate and potentially transport microplastics. As eddies are known to congregate nutrients and organisms, this phenomenon should be considered with regards to the potential impact of plastic pollution on the ecosystem in the open ocean. [ABSTRACT FROM AUTHOR]

There is growing global concern over the chemical, biological and ecological impact of plastics in the ocean. Remote sensing has the potential to provide long-term, global monitoring but for marine plastics it is still in its early stages. Some progress has been made in hyperspectral remote sensing of marine macroplastics in the visible (VIS) to short wave infrared (SWIR) spectrum. We present a reflectance model of sunlight interacting with a sea surface littered with macro plastics, based on geometrical optics and the spectral signatures of plastic and seawater. This is a first step towards the development of a remote sensing algorithm for marine plastic using light reflectance measurements in air. Our model takes the colour, transparency, reflectivity and shape of plastic litter into account. This concept model can aid the design of laboratory, field and Earth observation measurements in the VIS-SWIR spectrum and explain the results. [ABSTRACT FROM AUTHOR]

The leakage of large plastic litter (macroplastics) into the ocean is a major environmental problem. A significant fraction of this leakage originates from coastal cities, particularly during extreme rainfall events. As coastal cities continue to grow, finding ways to reduce this macroplastic leakage is extremely pertinent. Here, we explore why and how coastal cities can reduce macroplastic leakages during extreme rainfall events. Using nine global cities as a basis, we establish that while cities actively create policies that reduce plastic leakages, more needs to be done. Nonetheless, these policies are economically, socially and environmentally cobeneficial to the city environment. While the lack of political engagement and economic concerns limit these policies, lacking social motivation and engagement is the largest limitation towards implementing policy. We recommend cities to incentivize citizen and municipal engagement with responsible usage of plastics, cleaning the environment and preparing for future extreme rainfall events. [ABSTRACT FROM AUTHOR]

Almost all organisms in the ocean are impacted by ocean currents. Hence, there is growing interest by marine ecologists in using objective methods to assess current drift and its implications for marine connectivity. Here, an online tool – hosted at adrift.org.au – is introduced that allows for a simple, quantitative assessment of drift patterns and transit time scales on the global scale. The tool is based on a statistical transition matrix representation of the observed trajectories of more than 15 thousand surface drifters. Users can select any point in the ocean and obtain the evolution of the probability density distribution for a tracer released at that point, both forward and backward in time, for a maximum interval of 10 years. It is envisioned that this tool will be used in research and teaching, especially where estimates of drift patterns and transit times are required quickly. [ABSTRACT FROM AUTHOR]

Highlights: [•] We quantify temporal resolution sensitivity up to 30-days of Lagrangian particles. [•] Divergence times are faster than intrinsic dispersion. [•] Divergence times are slower than interannual variability associated dispersion. [•] Connectivity transport increase and transit time decrease in high dispersion flows. [•] Up to nine-day averaging show no significant degradation in connectivity. [Copyright &y& Elsevier]

Abstract: Following the March 2011 Fukushima disaster, large amounts of water contaminated with radionuclides, including Cesium-137, were released into the Pacific Ocean. With a half-life of 30.1 years, Cs-137 has the potential to travel large distances within the ocean. Using an ensemble of regional eddy-resolving simulations, this study investigates the long-term ventilation pathways of the leaked Cs-137 in the North Pacific Ocean. The simulations suggest that the contaminated plume would have been rapidly diluted below 10,000Bq/m3 by the energetic Kuroshio Current and Kurushio Extension by July 2011. Based on our source function of 22 Bq/m3, which sits at the upper range of the published estimates, waters with Cs-137 concentrations >10Bq/m3 are projected to reach the northwestern American coast and the Hawaiian archipelago by early 2014. Driven by quasi-zonal oceanic jets, shelf waters north of 45°N experience Cs-137 levels of 10–30Bq/m3 between 2014 and 2020, while the Californian coast is projected to see lower concentrations (10–20Bq/m3) slightly later (2016–2025). This late but prolonged exposure is related to subsurface pathways of mode waters, where Cs-137 is subducted toward the subtropics before being upwelled from deeper sources along the southern Californian coast. The model suggests that Fukushima-derived Cs-137 will penetrate the interior ocean and spread to other oceanic basins over the next two decades and beyond. The sensitivity of our results to uncertainties in the source function and to inter-annual to multi-decadal variability is discussed. [Copyright &y& Elsevier]

Abstract: Estimating the magnitude of Agulhas leakage, the volume flux of water from the Indian to the Atlantic Ocean, is difficult because of the presence of other circulation systems in the Agulhas region. Indian Ocean water in the Atlantic Ocean is vigorously mixed and diluted in the Cape Basin. Eulerian integration methods, where the velocity field perpendicular to a section is integrated to yield a flux, have to be calibrated so that only the flux by Agulhas leakage is sampled. Two Eulerian methods for estimating the magnitude of Agulhas leakage are tested within a high-resolution two-way nested model with the goal to devise a mooring-based measurement strategy. At the GoodHope line, a section halfway through the Cape Basin, the integrated velocity perpendicular to that line is compared to the magnitude of Agulhas leakage as determined from the transport carried by numerical Lagrangian floats. In the first method, integration is limited to the flux of water warmer and more saline than specific threshold values. These threshold values are determined by maximizing the correlation with the float-determined time series. By using the threshold values, approximately half of the leakage can directly be measured. The total amount of Agulhas leakage can be estimated using a linear regression, within a 90% confidence band of 12Sv. In the second method, a subregion of the GoodHope line is sought so that integration over that subregion yields an Eulerian flux as close to the float-determined leakage as possible. It appears that when integration is limited within the model to the upper 300m of the water column within 900km of the African coast the time series have the smallest root-mean-square difference. This method yields a root-mean-square error of only 5.2Sv but the 90% confidence band of the estimate is 20Sv. It is concluded that the optimum thermohaline threshold method leads to more accurate estimates even though the directly measured transport is a factor of two lower than the actual magnitude of Agulhas leakage in this model. [Copyright &y& Elsevier]

Primary productivity is limited by the availability of iron over large areas of the global ocean. Changes in the supply of iron to these regions could have major impacts on primary productivity and the carbon cycle. However, source regions and supply mechanisms of iron to the global oceans remain poorly constrained. Shelf sediments are considered one of the largest sources of dissolved iron to the global ocean, and a large shelf sediment iron flux is prescribed in many biogeochemical models over all areas of bathymetry shallower than 1000 m. Here, we infer the likely location of shelf sediment iron sources in the Southern Ocean, by identifying where satellite chlorophyll concentrations are enhanced over shallow bathymetry (<1000 m). We further compare chlorophyll concentrations with the position of ocean fronts, to assess the relative role of horizontal advection and upwelling for supplying iron to the ocean surface. We show that mean annual chlorophyll concentrations are not visibly enhanced over areas of shallow bathymetry that are located more than 500 km from a coastline. Mean annual chlorophyll concentrations >2 mg m −3 are only found within 50 km of a continental or island coastline. These results suggest that sedimentary iron sources only exist on continental and island shelves. Large sedimentary iron fluxes do not seem present on seamounts and submerged plateaus. Large chlorophyll blooms develop where the western boundary currents detach from the continental shelves, and turn eastward into the Sub-Antarctic Zone. Chlorophyll concentrations are enhanced along contours of sea surface height extending off the continental shelves, as shown by the trajectories of virtual water parcels in satellite altimetry data. These analyses support the hypothesis that bioavailable iron from continental shelves is entrained into western boundary currents, and advected into the Sub-Antarctic Zone along the Dynamical Subtropical Front. Our results indicate that upwelling at fronts in the open ocean is unlikely to deliver iron to the ocean surface from deep sources. Finally, we hypothesise how a reduction in sea level may have altered the distribution of shelf sediment iron sources in the Southern Ocean and increased export production over the Sub-Antarctic Zone during glacial intervals. [ABSTRACT FROM AUTHOR]

Abstract: Pelagic organisms'' movement and motion of buoyant particles are driven by processes operating across multiple, spatial and temporal scales. We developed a probabilistic, multi-scale model, the Connectivity Modeling System (CMS), to gain a mechanistic understanding of dispersion and migration processes in the ocean. The model couples offline a new nested-grid technique to a stochastic Lagrangian framework where individual variability is introduced by drawing particles'' attributes at random from specified probability distributions of traits. This allows 1) to track seamlessly a large number of both actively swimming and inertial particles over multiple, independent ocean model domains and 2) to generate ensemble forecasts or hindcasts of the particles'' three dimensional trajectories, dispersal kernels, and transition probability matrices used for connectivity estimates. In addition, CMS provides Lagrangian descriptions of oceanic phenomena (advection, dispersion, retention) and can be used in a broad range of oceanographic applications, from the fate of pollutants to the pathways of water masses in the global ocean. Here we describe the CMS modular system where particle behavior can be augmented with specific features, and a parallel module implementation simplifies data management and CPU intensive computations associated with solving for the tracking of millions of active particles. Some novel features include on-the-fly data access of operational hydrodynamic models, individual particle variability and inertial motion, and multi-nesting capabilities to optimize resolution. We demonstrate the performance of the interpolation algorithm by testing accuracy in tracing the flow stream lines in both time and space and the efficacy of probabilistic modeling in evaluating the bio-physical coupling against empirical data. Finally, following recommended practices for the development of community models, we provide an open source code with a series of coupled standalone, optional modules detailed in a user''s guide. [Copyright &y& Elsevier]

Plastic marine pollution is an increasing threat to global marine diversity. Quantifying this threat is particularly difficult and complex, especially when evaluating multiple species with different ecological requirements. Here, we examine the semi-enclosed basin of the Mediterranean Sea where the inputs of plastic pollution and its impact on marine diversity are still widely unknown. Eighty-four species from six taxonomic classes were evaluated to assess the risk of ingesting plastic marine debris, integrating inter-specific factors such as plastic exposure rates and life history traits (e.g., motility, habitat, and body size). Species were modelled within a spatial context to identify and estimate their exposure to plastic ingestion across the Mediterranean Sea using literature data, species distribution maps and plastic dispersion models. Our approach identified hotspots for the risk of plastic ingestion across multiple taxa in the Mediterranean Sea, highlighting that coastal species are at higher risk of ingesting plastic in the marine environment than open-sea species. The plastic exposure analysis indicated that species with larger home ranges were more at risk of exposure with increased distances while local species were more likely to be exposed to plastic closer to the centre of their home range location. The approach used in this study can be applied to support management and mitigation efforts throughout the Mediterranean Sea and in other geographic regions to minimize the impact of plastic pollution on marine diversity. Unlabelled Image • Mediterranean marine diversity is at high risk of plastic exposure. • A signal regression improves modelling exposure to plastic debris. • Species' homerange and life history traits predicted plastic ingestion. • Coastal areas are hotspots for plastic ingestion. [ABSTRACT FROM AUTHOR]

In this study, we assess the accuracy of a combined geostrophic and Ekman current product (GlobCurrent) that estimates ocean currents at 15 m depth, by coupling it to a synthetic particle tracking tool and comparing the virtual trajectories to those of surface drifting buoys drogued at 15 m in the Greater Agulhas Current Region. The velocities from a total of 1041 drifters are compared and evaluated to the synthetic particle-derived velocities for the period 1993–2015. On average the GlobCurrent underestimates the velocity in the Greater Agulhas Current by approximately 27%. The underestimation ranges from 4 to 64% in different regions, with the smallest error found in the Agulhas retroflection region, and the highest in the Benguela Upwelling System. Furthermore, we compare the time taken for the separation between the virtual and real drifters to reach 35 km. The mean separation time was found to be 78 h, with the shortest time (35 h) found in the Agulhas Current and the longest time (116 h) located in the Agulhas Return Current. Deploying 10,000 virtual drifters in a 1° × 1° box within the southern Agulhas Current shows a convergence of trajectories towards the core of the current, while higher divergence is evident in the Agulhas retroflection. To evaluate the utility of this synthetic particle tracking tool coupled with GlobCurrent in open ocean search and rescue operations, two test cases are examined: (1) a capsized catamaran spotted south of Cape Recife and recovered 5 days later south of Cape Agulhas; and (2) a drifter trajectory in the same region. The comparison suggests that the GlobCurrent forced synthetic particle tracking tool is not appropriate for predicting the trajectory of a capsized catamaran that does not have the same drift characteristics as a surface drifting buoy drogued to 15 m. [ABSTRACT FROM AUTHOR]

The distribution of marine species is often modeled using Eulerian approaches, in which changes to population density or abundance are calculated at fixed locations in space. Conversely, Lagrangian, or individual-based, models simulate the movement of individual particles moving in continuous space, with broader-scale patterns such as distribution being an emergent property of many, potentially adaptive, individuals. These models offer advantages in examining dynamics across spatiotemporal scales and making comparisons with observations from individual-scale data. Here, we introduce and describe such a model, the Individual-based Kinesis , Advection and Movement of Ocean ANimAls model (Ikamoana), which we use to replicate the movement processes of an existing Eulerian model for marine predators (the Spatial Ecosystem and Population Dynamics Model, SEAPODYM). Ikamoana simulates the movement of either individual or groups of animals by physical ocean currents, habitat-dependent stochastic movements (kinesis), and taxis movements representing active searching behaviours. Applying our model to Pacific skipjack tuna ( Katsuwonus pelamis ), we show that it accurately replicates the evolution of density distribution simulated by SEAPODYM with low time-mean error and a spatial correlation of density that exceeds 0.96 at all times. We demonstrate how the Lagrangian approach permits easy tracking of individuals’ trajectories for examining connectivity between different regions, and show how the model can provide independent estimates of transfer rates between commonly used assessment regions. In particular, we find that retention rates in most assessment regions are considerably smaller (up to a factor of 2) than those estimated by this population of skipjack’s primary assessment model. Moreover, these rates are sensitive to ocean state (e.g. El Nino vs La Nina) and so assuming fixed transfer rates between regions may lead to spurious stock estimates. A novel feature of the Lagrangian approach is that individual schools can be tracked through time, and we demonstrate that movement between two assessment regions at broad temporal scales includes extended transits through other regions at finer-scales. Finally, we discuss the utility of this modeling framework for the management of marine reserves, designing effective monitoring programmes, and exploring hypotheses regarding the behaviour of hard-to-observe oceanic animals. [ABSTRACT FROM AUTHOR]

Studying oceanography by using Lagrangian simulations has been adopted for a range of scenarios, such as the determining the fate of microplastics in the ocean, simulating the origin locations of microplankton used for palaeoceanographic reconstructions, and for studying the impact of fish aggregation devices on the migration behaviour of tuna. These simulations are complex and represent a considerable runtime effort to obtain trajectory results, which is the prime motivation for enhancing the performance of Lagrangian particle simulators. This paper assesses established performance enhancing techniques from Eulerian simulators in light of computational conditions and demands of Lagrangian simulators. A performance enhancement strategy specifically targeting physics-based Lagrangian particle simulations is outlined to address the performance gaps, and techniques for closing the performance gap are presented and implemented. Realistic experiments are derived from three specific oceanographic application scenarios, and the suggested performance-enhancing techniques are benchmarked in detail, so to allow for a good attribution of speed-up measurements to individual techniques. The impacts and insights of the performance enhancement strategy are further discussed for Lagrangian simulations in other geoscience applications. The experiments show that I/O-enhancing techniques, such as dynamic loading and buffering, lead to considerable speed-up on-par with an idealised parallelisation of the process over 20 nodes. Conversely, while the cache-efficient structure-of-arrays collection yields a visible speed-up, other alternative data structures fail in fulfilling the theoretically-expected performance increase. This insight demonstrates the importance of good data alignment in memory and caches for Lagrangian physics simulations. • Best practices for speeding up Eulerian flow studies are not transferable to Langrangian cases. • A performance-boosting strategy is adapted to the physical needs and computational conditions. • The input–output-bound performance of Lagrangian cases benefits from I/O reduction techniques. • Cache alignment of simulated entities, such as tracer particles, is key to an optimised CPU utilisation for the simulation. • Our performance enhancement leads to a peak speed-up of 21.5 for a many-field, complex biofouling simulation scenario. [ABSTRACT FROM AUTHOR]

Catch and distribution of tuna in the ocean are typically investigated with ocean basin-scale models. Due to their large scale, such models must greatly simplify tuna behaviour occurring at a scale below ∼ 100 km, despite interactions at this level potentially being important to both catch and distribution of tuna. For example, the associative behaviour of tuna with man-made floating objects, that are deployed by fishers to improve their catch rates (Fish Aggregating Devices; FADs), are usually ignored or simplified. Here we present a model that can be used to investigate the influence of tuna dynamics below the ∼ 100 km scale on larger scales. It is an Individual-Based Model (IBM) of a hypothetical, tuna-like species, that includes their interactions with each other, free-floating FADs and prey. In this IBM, both tuna and FADs are represented by Lagrangian particles that are advected by an ocean flow field, with tuna also exhibiting active swimming based on internal states such as stomach fullness. We apply the IBM in multiple configurations of idealized flow and prey fields, alongside differing interaction strengths between agents. When tuna swimming behaviour is influenced equally by prey and FADs, we find that the model simulations compare well with observations at the ≲ 100 km scale. For instance, compared to observations, tuna particles have a similar stomach fullness when associated or non-associated to a FAD, tuna colonize at similar timescales at FADs after their deployment and tuna particles exhibit similar variations in continuous residence times. However, we find large differences in emergent dynamics such as residence and catch among different flow configurations, because the flow determines the time scale at which tuna encounter FADs. These findings are discussed in the context of directing future research, and an improved interpretation of tuna catch and other data for the sustainable management of these economically important species. • We present a model of tuna, and their distribution and catch below the 100 km scale. • Simulations resemble observed tuna colonization at FADs of ∼ 60–80 days. • Stomach fullness is higher for tuna particles when not associated to a FAD, similar to observations. • Both observed and modelled tuna residence times at FADs are often 1–10 days and sometimes tens of days. • Ocean flow has a relevant impact on tuna-FAD interactions. [ABSTRACT FROM AUTHOR]

The pathways of recently ventilated North Atlantic Deep Water (NADW) are part of the lower limb of the Atlantic Meridional Overturning Circulation (AMOC). In the South Atlantic these pathways have been the subject of discussion for years, mostly due to the lack of observations. Knowledge of the pathways of the AMOC in the South Atlantic is a first order prerequisite for understanding the fluxes of climatically important properties. In this paper, historical and new observations, including hydrographic and oxygen sections, Argo data, and chlorofluorocarbons (CFCs), are examined together with two different analyzes of the Ocean general circulation model For the Earth Simulator (OFES) to trace the pathway of the recently ventilated NADW through the South Atlantic. CLIVAR-era CFCs, oxygen and salinity clearly show that the strongest NADW pathway in the South Atlantic is along the western boundary (similar to the North Atlantic). In addition to the western boundary pathway, tracers show an eastward spreading of NADW between ~17 and 25°S. Analyzed together with the results of earlier studies, the observations and model output presented here indicate that after crossing the equator, the Deep Western Boundary Current (DWBC) transports water with the characteristics of NADW and a total volume transport of approximately 14 Sv (1 Sv=10 6 m 3 s − 1 ). It crosses 5°S as a narrow western boundary current and becomes dominated by eddies further south. When this very energetic eddying flow reaches the Vitória-Trindade Ridge (~20°S), the flow follows two different pathways. The main portion of the NADW flow continues along the continental shelf of South America in the form of a strong reformed DWBC, while a smaller portion, about 22% of the initial transport, flows towards the interior of the basin. [ABSTRACT FROM AUTHOR]

The summertime phytoplankton bloom near the Kerguelen Plateau is in marked contrast to the low-chlorophyll conditions typical of the Southern Ocean and is thought to arise from natural iron fertilisation. The mechanisms of iron supply to the euphotic zone in this region are poorly understood, and numerical studies of iron transport have until now omitted fine-scale (sub-mesoscale) dynamics which have been shown to significantly increase vertical transport in other parts of the ocean. We present the first sub-mesoscale-resolving study of the flow and vertical transport in this region. The modelled transport and flow structure agree well with observations. We find that an increase in horizontal resolution from mesoscale-resolving (1/20°) to 1/80° resolves sub-mesoscale filamentary frontal structures in which vertical velocities are dramatically higher and are consistent with available observations. Lagrangian tracking shows that water is advected to the surface from much greater depth in the sub-mesoscale-resolving experiment, and that vertical exchange is far more rapid and frequent. This study of sub-mesoscale vertical velocities sets the foundation for subsequent investigation of iron transport in this environment. [ABSTRACT FROM AUTHOR]

Abstract: Five years of data from a line of dynamic height moorings (DHM), bottom-pressure recorders (BPR), and pressure-equipped inverted echo sounders (PIES) near the Atlantic Ocean western boundary at 26.5°N are used to evaluate the structure and variability of the Deep Western Boundary Current (DWBC) during 2004–2009. Comparisons made between transports estimated from the DHM+BPR and those made by the PIES demonstrate that the two systems are collecting equivalent volume transport information (correlation coefficient r=0.96, root-mean-square difference=6Sv; 1Sv=106 m3 s−1). Integrated to ∼450km off from the continental shelf and between 800 and 4800dbar, the DWBC has a mean transport of approximately 32Sv and a standard deviation during these five years of 16Sv. Both the barotropic (full-depth vertical mean) and baroclinic flows have significant variability (changes exceeding 10Sv) on time scales ranging from a few days to months, with the barotropic variations being larger and more energetic at all time scales. The annual cycle of the deep transport is highly dependent on the horizontal integration distance; integrating ∼100km offshore yields an annual cycle of roughly similar magnitude but shifted in phase relative to that found from current meter arrays in the 1980–1990s, while the annual cycle becomes quite weak when integrating ∼450km offshore. Variations in the DWBC transport far exceed those of the total basin-wide Meridional Overturning Circulation (standard deviations of 16Sv vs. 5Sv). Transport integrated in the deep layer out to the west side of the Mid-Atlantic Ridge still demonstrates a surprisingly high variance, indicating that some compensation of the western basin deep variability must occur in the eastern basin. [Copyright &y& Elsevier]