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The phenology, distribution, and size composition of plankton communities are changing rapidly in response to warming. This may lead to shifts in the prey fields of planktivorous fish, which play a key role in transferring energy up marine food chains. Here, we use 60 + years of Continuous Plankton Recorder data to explore temporal trends in key taxa and community traits in the prey field of planktivorous lesser sandeels (Ammodytes marinus) in the North Sea, the Faroes and southern Iceland. We found marked spatial variation in the prey field, with Calanus copepods generally being much more common in the northern part of the study area. In the western North Sea, the estimated amount of available energy in the prey field has decreased by more than 50% since the 1960s. This decrease was accompanied by declining abundances of small copepods, and shifts in the timing of peak annual prey abundances. Further, the estimated average prey community body size has increased in several of the locations considered. Overall, our results point to the importance of regional studies of prey fields, and caution against inferring ecological consequences based only on large-scale trends in key taxa or mean community traits.

1. We present StrathE2E2, an R package for modelling the whole ecosystem, or ‘big-picture’ effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs. 2. StrathE2E2 has two linked parts – a fishing fleet model and an ecology model. The fishing model combines harvesting, discarding and seabed disturbance rates across a range of gears and passes the results into the ecology model. 3. The ecology model is a network of coupled ordinary differential equations representing the rates of change in nitrogen mass of organic detritus, dissolved inorganic nutrient, and coarse guilds of living biomass spanning microbes to megafauna. The equations include representations of feeding, metabolism, reproduction, active migrations, advection and mixing. Environmental driving data include temperature, irradiance, hydrodynamics, and nutrient inputs from rivers, atmosphere and ocean boundaries. 4. The package includes functions for parameter optimization, global sensitivity analysis, and Monte Carlo estimation of credible intervals for model outputs 5. A fully developed and documented implementation for the North Sea is included with the package.

Synchrony in demographic rates between spatially disjunct populations is a widespread phenomenon, although the underlying mechanisms are often not known. This synchrony and its spatial patterns can have important consequences for the long-term persistence of metapopulations and can also be used to infer drivers of population dynamics. Here, we examined spatial patterns of synchrony in the breeding success of black-legged kittiwakes Rissa tridactyla in the UK, using an extensive dataset on kittiwake breeding success and 2 different ways of measuring synchrony: one reflecting synchrony in inter-annual fluctuations only (rdiff) and one reflecting synchrony in both inter-annual fluctuations and long-term trends (r). We found that between-colony synchrony in breeding success decreased with distance up to just over 200 km but that some colony pairs showed stronger or weaker synchrony than expected based on distance. This was also reflected in the configuration of spatially coherent clusters of kittiwake colonies with synchronous breeding success. Further, we compared the support for different drivers of these spatial patterns, including trophic interactions and weather conditions. We found that the spatial dynamics of the kittiwakes’ main prey in this region, the lesser sandeel Ammodytes marinus, appeared to play some role in generating synchrony in long-term patterns, but their role in generating synchrony in inter-annual fluctuations was less clear. The study shows that examining spatial patterns in synchrony can provide useful information for inferring potential drivers and the spatial scale over which they are acting.

Funidng: This study was supported by the Changing Arctic Ocean project MiMeMo (NE/R012679/1) jointly funded by the UKRI Natural Environment Research Council (NERC) and the German Federal Ministry of Education and Research (BMBF/03F0801A). Brierley was also supported by ArcticPRIZE (NE/P005721/1). Projecting the consequences of warming and sea-ice loss for Arctic marine food web and fisheries is challenging due to the intricate relationships between biology and ice. We used StrathE2EPolar, an end-to-end (microbes-to-megafauna) food web model incorporating ice-dependencies to simulate climate-fisheries interactions in the Barents Sea. The model was driven by output from the NEMO-MEDUSA earth system model, assuming RCP 8.5 atmospheric forcing. The Barents Sea was projected to be > 95% ice-free all year-round by the 2040s compared to > 50% in the 2010s, and approximately 2 °C warmer. Fisheries management reference points (FMSY and BMSY) for demersal fish (cod, haddock) were projected to increase by around 6%, indicating higher productivity. However, planktivorous fish (capelin, herring) reference points were projected to decrease by 15%, and upper trophic levels (birds, mammals) were strongly sensitive to planktivorous fish harvesting. The results indicate difficult trade-offs ahead, between harvesting and conservation of ecosystem structure and function. Publisher PDF

The spring phytoplankton bloom is a key event in temperate and polar seas, yet the mechanisms that trigger it remain under debate. Some hypotheses claim that the spring bloom onset occurs when light is no longer limiting, allowing phytoplankton division rates to surpass a critical threshold. In contrast, the Disturbance Recovery Hypothesis (DRH) proposes that the onset responds to an imbalance between phytoplankton growth and loss processes, allowing phytoplankton biomass to start accumulating, and this can occur even when light is still limiting. Although several studies have shown that the DRH can explain the spring bloom onset in oceanic waters, it is less certain whether and how it also applies to coastal areas. To address this question at a coastal location in the Scottish North Sea, we combined 21 years (1997–2017) of weekly in situ chlorophyll and environmental data with meteorological information. Additionally, we also analyzed phytoplankton cell counts estimated using microscopy (2000–2017) and flow cytometry (2015–2017). The onset of phytoplankton biomass accumulation occurred around the same date each year, 16 ± 11 d (mean ± SD) after the winter solstice, when light limitation for growth was strongest. Also, negative and positive biomass accumulation rates (r) occurred respectively before and after the winter solstice at similar light levels. The seasonal change from negative to positive r was mainly driven by the rate of change in light availability rather than light itself. Our results support the validity of the DRH for the studied coastal region and suggest its applicability to other coastal areas.

Projecting ocean biogeochemistry and fisheries resources under climate change requires confidence in simulation models. Core to such models is the description of consumer dynamics relating prey abundance to capture, digestion efficiency and growth rate. Capture is most commonly described as a linear function of prey encounter or by rectangular hyperbola. Most models also describe consumers as eating machines which “live-to-eat,” where growth (μ) is limited by a maximum grazing rate (Gmax). Real consumers can feed much faster than needed to support their maximum growth rate (μmax); with feeding modulated by satiation, they “eat-to-live.” A set of strategic analyses were conducted of these alternative philosophies of prey consumption dynamics and testing of their effects in the StrathE2E end-to-end marine food web and fisheries model. In an experiment where assimilation efficiencies were decreased by 10%, such as might result from a change in temperature or ocean acidity, the different formulation resulted in up to 100% variation in the change in abundances of food web components, especially in the mid-trophic levels. Our analysis points to a need for re-evaluation of some long-accepted principles in consumer-resource modeling.

The boreal copepod Calanus finmarchicus accumulates lipid reserves during summer feeding in surface ocean waters, which enable it to stay at depth and survive famine during overwintering. Respiration of lipids during prolonged overwintering at ocean depths (> 1000 m in some areas) has been shown to result in a net sequestration of carbon into the deep ocean: the so-called “lipid pump.” Here, we provide a comprehensive synthesis of the geographic and vertical variations in lipid content of overwintering animals across the Subpolar Eastern North Atlantic and, on the basis of this, we revise the estimates of carbon sequestration. Wax ester content ranged from 40 to 190 μg individual−1 at > 250 m depths, with highest concentrations in the coldest (< 0C) waters at 400–600 m depth at the slope east of Faroe Islands and east of Greenland and lowest in the warmer (> 4C) Irminger Sea and Rockall Basin. Our new analysis results in about 44% higher estimates of carbon sequestration at up to 11.5 g C m−2

High quality quantitative maps of seabed sedimentary physical and geochemical properties have numerous research and conservation applications, including habitat and ecosystem modelling, marine spatial planning and ecosystem service mapping. However, such maps are lacking for many ecologically and economically important marine areas. Using legacy data supplemented by measurements from recent benthic surveys, modelled hydrodynamic variables and high resolution bathymetry, quantitative maps for the top 10 cm of seabed sediment were generated via a combination of statistical and machine-learning techniques for the Firth of Clyde, a semi-enclosed coastal sea on the west coast of Scotland. The maps include sediment fractions of mud, sand and gravel, whole-sediment median grain size, sediment permeability and porosity, rates of natural seabed abrasion, and sediment particulate organic carbon and nitrogen content. Properties were mapped over an unstructured grid, so that very high resolutions were achieved close to the coastlines, where sediments may be expected to be spatially heterogeneous. Overall, the maps reveal extensive areas of very low sediment permeability coupled with low rates of natural seabed disturbance. Moreover, muddy sediments in the inner Firth of Clyde, Inchmarnock Water and the sea lochs are enriched in organic carbon and nitrogen relative to the sediments of the outer Firth of Clyde. As a demonstration of the value of these maps, the standing stock of organic carbon and nitrogen in the surficial sediments of the Clyde was calculated. The Clyde stores 3.42 and 0.33 million tonnes of organic carbon and nitrogen in the top 10 cm of seabed sediment, respectively, substantially contributing to Scotland’s coastal and shelf blue carbon stocks. Data products are available from: https://doi.org/10.15129/2003faa2-ee93-4c11-bb16-48485f5f136d.

Rising temperatures are melting the ice that covers the Arctic Ocean, allowing sunlight into waters that have been dark for thousands of years. Previously barren ice-covered regions are being transformed into productive seas. In this article, we explain how computer modeling can be used to predict how this transformation will affect the food web that connects plankton to fish and top predators, like whales and polar bears. Images of starving polar bears have become symbolic of the effects of the warming climate. Melting of the sea-ice is expected to reduce the bears’ ability to hunt for seals. However, at the same time, the food web upon which bears depend is becoming more productive, so it is not completely clear what the eventual outcome will be. Computer models help us to understand these systems and help us make policy decisions about the management of newly available Arctic resources.

Viruses play critical roles in the dynamics of microbial communities. Lytic viruses, for example, kill significant proportions of autotrophic and heterotrophic microbes. The dynamic interplay between viruses and microbes results from an overlap of physiological, ecological, and evolutionary responses: environmental changes trigger host physiological changes, affecting the ecological interactions of host and virus and, ultimately, the evolutionary pressures influencing the two populations. Recent theoretical work studied how the dependence of viral traits on host physiology (viral plasticity) affects the evolutionarily stable host cell size and viral infection time emerging from coevolution. Here, we broaden the scope of the framework to consider any coevolutionary outcome, including potential evolutionary collapses of the system. We used the case study of Escherichia coli and T-like viruses under chemo-stat conditions, but the framework can be adapted to any microbe-virus system. Oligotrophic conditions led to smaller, lower-quality but more abundant hosts, and infections that were longer but produced a reduced viral offspring. Conversely, eutrophic conditions resulted in fewer but larger higher-quality hosts, and shorter but more productive infections. The virus influenced host evolution decreasing host radius more noticeably for low than for high dilution rates, and for high than for low nutrient input concentration. For low dilution rates, the emergent infection time minimized host need/use, but higher dilution led to an opportunistic strategy that shortened the duration of infections. System collapses driven by evolution resulted from host failure to adapt quickly enough to the evolving virus. Our results contribute to understanding the eco-evolutionary dynamics of microbes and virus, and to improving the predictability of current models for host-virus interactions. The large quantitative and qualitative differences observed with respect to a classic description (in which viral traits are assumed to be constant) highlights the importance of including viral plasticity in theories describing short- and long-term host-virus dynamics.

When making predictions about ecosystems, we often have available a number of different ecosystem models that attempt to represent their dynamics in a detailed mechanistic way. Each of these can be used as a simulator of large-scale experiments and make projections about the fate of ecosystems under different scenarios in order to support the development of appropriate management strategies. However, structural differences, systematic discrepancies and uncertainties lead to different models giving different predictions. This is further complicated by the fact that the models may not be run with the same functional groups, spatial structure or time scale. Rather than simply trying to select a 'best' model, or taking some weighted average, it is important to exploit the strengths of each of the models, while learning from the differences between them. To achieve this, we construct a flexible statistical model of the relationships between a collection of mechanistic models and their biases, allowing for structural and parameter uncertainty and for different ways of representing reality. Using this statistical meta-model, we can combine prior beliefs, model estimates and direct observations using Bayesian methods, and make coherent predictions of future outcomes under different scenarios with robust measures of uncertainty. In this paper we take a diverse ensemble of existing North Sea ecosystem models and demonstrate the utility of our framework by applying it to answer the question what would have happened to demersal fish if fishing was to stop.

Seabed sediment mapping is important for a wide range of marine policy, planning and scientific issues, and there has been considerable national and international investment around the world in the collation and synthesis of sediment datasets. However, in Europe at least, much of this effort has been directed towards seabed classification and mapping of discrete habitats. Scientific users often have to resort to reverse engineering these classifications to recover continuous variables, such as mud content and median grain size, that are required for many ecological and biophysical studies. Here we present a new set of 0.125∘ by 0.125∘ resolution synthetic maps of continuous properties of the north-west European sedimentary environment, extending from the Bay of Biscay to the northern limits of the North Sea and the Faroe Islands. The maps are a blend of gridded survey data, statistically modelled values based on distributions of bed shear stress due to tidal currents and waves, and bathymetric properties. Recent work has shown that statistical models can predict sediment composition in British waters and the North Sea with high accuracy, and here we extend this to the entire shelf and to the mapping of other key seabed parameters. The maps include percentage compositions of mud, sand and gravel; porosity and permeability; median grain size of the whole sediment and of the sand and the gravel fractions; carbon and nitrogen content of sediments; percentage of seabed area covered by rock; mean and maximum depth-averaged tidal velocity and wave orbital velocity at the seabed; and mean monthly natural disturbance rates. A number of applications for these maps exist, including species distribution modelling and the more accurate representation of sea-floor biogeochemistry in ecosystem models. The data products are available from https://doi.org/10.15129/1e27b806-1eae-494d-83b5-a5f4792c46fc.

Assessments of many West African fish stocks rely on fishery dependent catch and effort data. Typically, these treat the catch data as error free and some assume that fishing power does not change over time. To address these issues we develop a fleet based surplus production model that accounts for increases in fishing power. It allows errors both in effort and catch data so avoiding the assumption that catch data are exact. Mean annual fleet fishing power increase can be estimated when data from multiple fleets are available provided it can be specified for at least one fleet. The model is tested using simulated data and then applied to western stocks of anchovy (Engraulis encrasicolus) and bonga shad (Ethmalosa fimbriata) in the Fishery Committee for the Eastern Central Atlantic (CECAF) area. Both stocks appear to be over-exploited and near to collapse. Corrections for fishing power are important in the anchovy assessment and help to explain conflicting trends in the data. Uncertainty in the assessments is explored with a range of sensitivity tests.

This article presents an introduction and overview of a modelling project “TeraWatt: Large scale interactive coupled 3D modelling for wave and tidal energy resource and environmental impact”. The project was funded by the SUstainable PowER GENeration (SUPERGEN) “Marine Hub”. SUPERGEN (http://www.rcuk.ac.uk/research/xrcprogrammes/energy/energyresearch/supergen) is an initiative of the Research Councils UK (RCUK) Energy Programme, led by the Engineering and Physical Sciences Research Council (EPSRC). It is focused on supporting resilient and sustainable generation, supply, transmission and storage of the UK's energy. The Marine Challenge addresses the UK Centre for Marine Energy Research's (UKCMER) mission to support the wave and tidal energy sector beyond their current state of development.

We describe a modelling project to estimate the potential effects of wave & tidal stream renewables on the marine environment. • Realistic generic devices to be used by those without access to the technical details available to developers are described. • Results show largely local sea bed effects at the level of the currently proposed renewables developments in our study area. • Large scale 3D modelling is critical to quantify the direct, indirect and cumulative effects of renewable energy extraction. • This is critical to comply with planning & environmental impact assessment regulations and achieve Good Environmental Status.

Seawater turbidity due to suspended particulate material (SPM) is an important property of a marine ecosystem, determining the underwater light environment and many aspects of biological production and ecology. SPM concentrations are largely determined by patterns of sediment resuspension from the seabed due to shear stress caused by waves and currents. Hence planning for the construction of large scale offshore structures which will alter regional hydrodynamics needs to consider the consequences for SPM concentrations. Here we develop a one-dimensional (vertical) model of SPM dynamics which can be used to scope the effects of changes in wave and tidal current properties at a site. We implement the model for a number of sites off the east coast of Scotland where we have extensive data sets to enable numerical parameter optimisation. The model performs well at simulating fluctuations in turbidity varying from flood-ebb tidal cycles, spring-neap cycles, storm wave events, and an annual cycle of SPM concentration which is attributed to seasonal consolidation of seabed sediments. Sensitivity analysis shows that, for the range of seabed sediment types in the study (water depth 16–50 m; mud content 0.006–0.380 proportion by weight), relatively large (50%) attenuations of tidal current speed are required to produce changes in water column turbidity which would be detectable by observations given the variability in measurements. The model has potential for application to map the large scale sensitivity of turbidity distributions to the installation of wave and tidal energy extraction arrays.

Data on Secchi disc depth (the depth at which a standard white disc lowered into the water just becomes invisible to a surface observer) show that water clarity in the North Sea declined during the 20th century, with likely consequences for marine primary production. However, the causes of this trend remain unknown. Here we analyse the hypothesis that changes in the North Sea's wave climate were largely responsible by causing an increase in the concentrations of suspended particulate matter (SPM) in the water column through the resuspension of seabed sediments. First, we analysed the broad-scale statistical relationships between SPM and bed shear stress due to waves and tides. We used hindcasts of wave and current data to construct a space–time dataset of bed shear stress between 1997 and 2017 across the northwest European Continental Shelf and compared the results with satellite-derived SPM concentrations. Bed shear stress was found to drive most of the inter-annual variation in SPM in the hydrographically mixed waters of the central and southern North Sea. We then used a long-term wave reanalysis to construct a time series of bed shear stress from 1900 to 2010. This shows that bed shear stress increased significantly across much of the shelf during this period, with increases of over 20 % in the southeastern North Sea. An increase in bed shear stress of this magnitude would have resulted in a large reduction in water clarity. Wave-driven processes are rarely included in projections of climate change impacts on marine ecosystems, but our analysis indicates that this should be reconsidered for shelf sea regions.

We examine long-term trends in the average growth rates and maturation schedules of herring and sprat populations using survey data collected from the North Sea and west of Scotland since the 1960s and 1980s respectively. Otolith age data and maturity data are used to calculate time series of mean lengths at age, von Bertalanffy growth parameters, and probabilistic maturation reaction norms. As the growth and maturation of fish is known to be influenced by temperature and stock abundances, we account for these variables using Generalised Additive Models. Each of the herring populations displayed either steady declines in mean length across multiple age groups, or declines in length followed years later by some recovery. Depending on region, lengths at age of sprat increased or decreased over time. Varying temporal trends in maturation propensity at age and length were observed across herring populations. Many of the trends in growth rate and maturation were correlated to population abundance and/or temperature. In general, abundance is shown to be negatively correlated to growth rates in herring and sprat, and positively correlated with maturation propensity in herring. Temperature is also shown to be correlated to growth and maturation, and although the effect is consistent within species, the temperature effects differ between herring and sprat. This study provides detailed information about long-term trends in growth and maturation, which is lacking for some of these pelagic stocks, especially in the west of Scotland.

Storm surges are an abnormal enhancement of the water level in response to weather perturbations. They have the capacity to cause damaging flooding of coastal regions, especially when they coincide with astronomical high spring tides. Some areas of the UK have suffered particularly damaging surge events, and the Firth of Clyde is a region with high risk due to its location and morphology. Here, we use a three-dimensional high spatial resolution hydrodynamic model to simulate the local bathymetric and morphological enhancement of surge in the Clyde, and disaggregate the effects of far-field atmospheric pressure distribution and local scale wind forcing of surges. A climatological analysis, based on 30 years of data from Millport tide gauges, is also discussed. The results suggest that floods are not only caused by extreme surge events, but also by the coupling of spring high tides with moderate surges. Water level is also enhanced by a funnelling effect due to the bathymetry and the morphology of fjordic sealochs and the River Clyde Estuary. In a world of rising sea level, studying the propagation and the climatology of surges and high water events is fundamental. In addition, high-resolution hydrodynamic models are essential to forecast extreme events and to prevent the loss of lives, or to plan coastal defences solutions.

Densely populated coastal areas of the North Sea are particularly vulnerable to severe wave conditions, which overtop or damage sea-defences leading to dangerous flooding. Around the shallow southern North Sea, where the coastal margin is low-lying and population density is high, oceanographic modelling has helped to develop forecasting systems to predict flood risk. However coastal areas of the deeper northern North Sea are also subject to regular storm damage but there has been little or no effort to develop coastal wave models for these waters. Here we present a high spatial resolution model of northeast Scottish coastal waters, simulating waves and the effect of tidal currents on wave propagation, driven by global ocean tides, far-field wave conditions, and local air pressure and wind stress. We show that the wave–current interactions and wave–wave interactions are particularly important for simulating the wave conditions close to the coast at various locations. The model can simulate the extreme conditions experienced when high (spring) tides are combined with sea-level surges and large Atlantic swell. Such a combination of extremes represents a high risk for damaging conditions along the Scottish coast.

Stereo-video scuba transects were conducted during daylight hours from June to September 2013 within a proposed marine protected area (MPA) in the Firth of Clyde, west of Scotland. More juvenile Atlantic cod Gadus morhua of fork length (LF) range 6–11 cm were observed in substrata containing mixed gravel, including maerl, than in boulder-cobble substrata with high algal cover, or sand with low density seagrass. Community composition was significantly different between substratum types. A decrease in G. morhua abundance was observed over the period of data collection. Over time, mean and variance in G. morhua LF increased, indicating multiple recruitment events. Protecting mixed gravel substrata could be a beneficial management measure to support the survival and recruitment of juvenile G. morhua; other substrata might be important at night given their diel migratory behaviour. Stereo-video cameras provide a useful non-destructive fisheries-independent method to monitor species abundance and length measurements.

Diapause plays a key role in the life cycle of high latitude zooplankton. During diapause, animals avoid starving in winter by living in deep waters where metabolism is lower and met by lipid reserves. Global warming is therefore expected to shorten the maximum potential diapause duration by increasing metabolic rates and by reducing body size and lipid reserves. This will alter the phenology of zooplankton, impact higher trophic levels and disrupt biological carbon pumps. Here, we project the impacts of climate change on the key North Atlantic copepod Calanus finmarchicus under IPCC RCP 8.5. Potential diapause duration is modelled in relation to body size and overwintering temperature. The projections show pronounced geographic variations. Potential diapause duration reduces by more than 30% in the Western Atlantic, whereas in the key overwintering centre of the Norwegian Sea it changes only marginally. Surface temperature rises, which reduce body size and lipid reserves, will have a similar impact to deep-water changes on diapause in many regions. Because deep-water warming lags that at the surface, animals in the Labrador Sea could offset warming impacts by diapausing in deeper waters. However, the ability to control diapause depth may be limited.

Phenotypic plasticity plays an important role in the survival of individuals. In microbial host-virus systems, previous studies have shown the stabilizing effect that host plasticity has on the coexistence of the system. By contrast, it remains uncertain how the dependence of the virus on the metabolism of the host (i.e. “viral plasticity”) shapes bacteria-phage population dynamics in general, or the stability of the system in particular. Moreover, bacteria-phage models that do not consider viral plasticity are now recognised as overly simplistic. For these reasons, here we focus on the effect of viral plasticity on the stability of the system under different environmental conditions. We compared the predictions from a standard bacteria-phage model, which neglects plasticity, with those of a modification that includes viral plasticity. We investigated under which conditions viral plasticity promotes coexistence, with or without oscillatory dynamics. Our analysis shows that including viral plasticity reveals coexistence in regions of the parameter space where models without plasticity predict a collapse of the system. We also show that viral plasticity tends to reduce population oscillations, although this stabilizing effect is not consistently observed across environmental conditions: plasticity may instead reinforce dynamic feedbacks between the host, the virus, and the environment, which leads to wider oscillations. Our results contribute to a deeper understanding of the dynamic control of bacteriophage on host populations observed in nature.

International audience; A scavenger is an animal that feeds on dead animals (carrion) that it has not killed itself. Fisheries discards are often seen as an important food source for marine scavengers so the reduction of discards due to the Landing Obligation may affect their populations. The literature on scavenging in marine ecosystems is considerable, due to its importance in the trophic ecology of many species. Although discards undoubtedly contribute to these species’ food sources, few can be seen to be solely dependent on carrion (including discards). Ecosystem models predicted that discards contributed very little to the diet of scavengers at a regional scale. A reduction in discards through the Landing Obligation may therefore affect populations for a few species in some areas, but generally this is unlikely to be the case. But it is challenging to identify how important discards might be to scavengers, as they are taxonomically diverse and vary in the role they play in scavenging interactions.

Marine legislation is becoming more complex and marine ecosystem-based management is specified in national and regional legislative frameworks. Shelf-seas community and ecosystem models (hereafter termed ecosystem models) are central to the delivery of ecosystem-based management, but there is limited uptake and use of model products by decision makers in Europe and the UK in comparison with other countries. In this study, the challenges to the uptake and use of ecosystem models in support of marine environmental management are assessed using the UK capability as an example. The UK has a broad capability in marine ecosystem modelling, with at least 14 different models that support management, but few examples exist of ecosystem modelling that underpin policy or management decisions. To improve understanding of policy and management issues that can be addressed using ecosystem models, a workshop was convened that brought together advisors, assessors, biologists, social scientists, economists, modellers, statisticians, policy makers, and funders. Some policy requirements were identified that can be addressed without further model development including: attribution of environmental change to underlying drivers, integration of models and observations to develop more efficient monitoring programmes, assessment of indicator performance for different management goals, and the costs and benefit of legislation. Multi-model ensembles are being developed in cases where many models exist, but model structures are very diverse making a standardised approach of combining outputs a significant challenge, and there is a need for new methodologies for describing, analysing, and visualising uncertainties. A stronger link to social and economic systems is needed to increase the range of policy-related questions that can be addressed. It is also important to improve communication between policy and modelling communities so that there is a shared understanding of the strengths and limitations of ecosystem models.

Probabilistic maturation reaction norms (PMRNs) were used to investigate the maturation schedules of cod, haddock and whiting in the Firth of Clyde to determine if typical lengths at maturation have changed significantly since 1986. Some potential sources of growth-independent plasticity were accounted for by including sea-surface temperature and abundance variables in the analysis. The PMRNs of the Clyde populations were compared with those from the wider west coast, in conjunction with regional differences in the fishery, to assess whether fishing may have been driving the observed trends of decreasing lengths at maturation. The lengths at which haddock, whiting and female cod were likely to mature decreased significantly during 1986–2009, with rates of change being particularly rapid in the Clyde. It was not possible to estimate PMRNs for male cod due to limited data. Trends in temperature and abundance were shown to have only marginal affects upon PMRN positions, so temporal trends in maturation schedules appear to have been due to a combination of plastic responses to other environmental variables and/or fishing. Regional differences in fishing intensity and the size-selectivity of the fisheries suggest that the decreases in lengths at maturation have been at least partially due to fishing. The importance and scale of the Clyde Nephrops fishery increased as demersal landings declined, and the majority of demersal fish landings have come from Nephrops bycatch since about 2005 when the demersal fishery ceased. Since it appears as though fishing may have caused increasingly early maturation, and a substantial Nephrops fishery continues to operate in the Clyde, reversal of these changes is likely to take a long time – particularly if there is an evolutionary component to the trends. If size-selective fishing has contributed to the lowered abundance of large fish by encouraging maturation at increasingly small lengths, then large fish may remain uncommon in the Clyde until the observed trends in maturation lengths reverse.

Here we present a new, pan-North-Atlantic compilation of data on key mesozooplankton species, including the most important copepod, Calanus finmarchicus. Distributional data of eight representative zooplankton taxa, from recent (2000–2009) Continuous Plankton Recorder data, are presented, along with basin-scale data of the phytoplankton colour index. Then we present a compilation of data on C. finmarchicus, including observations of abundance, demography, egg production and female size, with accompanying data on temperature and chlorophyll. This is a contribution by Canadian, European and US scientists and their institutions: http://doi.pangaea.de/10.1594/PANGAEA.820732, http://doi.pangaea.de/10.1594/PANGAEA.824423, http://doi.pangaea.de/10.1594/PANGAEA.828393 (please also see Melle et al., 2013; Castellani and Licandro, 2013; Jónasdóttir et al., 2014).

The important calanoid copepod species Calanus finmarchicus and C. helgolandicus have distinct geographic ranges which are changing under the influence of climate change. Understanding the mechanisms underlying their distributions is becoming increasingly important as a result of the possible ecological impacts of these range shifts. Here we review inter-species differences in key life cycle traits that influence each species’ geographic distribution, in particular development and growth, fecundity, feeding behaviour, vertical migration and overwintering behaviour. The distinct temperature niche of each species leads to an a priori assumption that the response of life cycle traits to temperature is a key determinant of their contrasting geographic distributions. A new development model was created to reconcile published experimental development times for each species. Model output indicates that at temperatures below approximately 12-13 ˚C, C. finmarchicus is the faster developing species, but above these temperatures C. helgolandicus develops more quickly. Conventionally Calanus development time is assumed to decrease monotonically with temperature; however our model indicates that the response of development time to temperature is instead U-shaped. Differences in life cycle aspects such as seasonality and vertical structuring are interpreted in light of this development model. Body size and lipid accumulation abilities could be significant influences on each species’ geographic distribution; however evidence is consistent with inter-species differences not existing for these traits. Published evidence shows that inter-species differences in egg production may exist, but do not follow a clear pattern. Diapause is an important and well studied life cycle adaptation of C. finmarchicus, but has received little attention in C. helgolandicus. We synthesised knowledge of diapause and suggest the hypothesis that C. helgolandicus is restricted to continental shelf regions as a result of an inability to diapause for significant periods. This synthesised view of each species’ respective life cycle traits is that response of growth and development to temperature is the only known difference between each species, which indicates a promising direction for the extension of population models of C. finmarchicus to C. helgolandicus.

Synthesis studies of fish stocks worldwide suggest improving status of mainly target species that are fully assessed. Other analyses, primarily based on catch data alone, but which include a wider range of species as well as bycatch, present a different view. Catch only analyses could be more robust if fishery independent data were used and discards accounted for. We develop a model that uses only survey biomass at length and landings data to estimate fishing mortality, spawning stock biomass (SSB) and discards. An analysis of species from the North Sea shows the model results compare well with most fully assessed stocks. When applied to bycatch species with limited data, trends in fishing mortality and SSB typically reflect those of the target species. In the last decade mean fishing mortality rates have tended to decline while mean spawning stock biomass (SSB) has increased. Despite increasing SSB, recent mean recruitment appears to have been lower than previously which may limit future biomass recovery. Species usually associated with more northerly distributions appear to show the greatest effect of weaker recruitment which may be linked to climate. Estimated discards have tended to decline in magnitude as a result of reduced fishing mortality and associated lower total catches. The model offers a simple way to use both landings and survey data to obtain more detailed population trends for data limited species.

This paper addresses relationships between the distribution and abundance of zooplankton and its habitat in the northern North Atlantic Ocean. Distributions of ten representative zooplankton taxa, from recent (2000-2009) Continuous Plankton Recorder data, are presented, along with basin-scale patterns of annual sea surface temperature and phytoplankton color. The distribution patterns represent the manifestation of very different physiological, life history and ecological interactions of each taxon with the North Atlantic habitat characteristics. The paper then focuses on a pan-Atlantic compilation of demographic and life history information for the planktonic copepod, Calanus finmarchicus, perhaps one of the most ecologically important and certainly the most studied zooplankton species in the North Atlantic. Abundance, dormancy, egg production and mortality in relation to temperature and phytoplankton biomass, using chlorophyll a as a proxy, are analyzed in the context of understanding factors involved in determining the distribution and abundance of C. finmarchicus across its range. Several themes emerge: (1) transport of C. finmarchicus is from the south to the north in the northeast Atlantic, but from the north to the south in the western North Atlantic, which has implications for understanding population responses to climate forcing on coastal shelves, , (2) recruitment to the youngest copepodite stages occurs during or just after the phytoplankton bloom in the east while it occurs after the bloom in many western sites, (3) while the deep basins in the Labrador Sea and Norwegian Sea are primary sources of C. finmarchicus production, the western North Atlantic marginal seas have an important role in sustaining high C. finmarchicus abundance on the western North Atlantic shelves, (4) differences in mean temperature and chlorophyll concentration between the western and eastern North Atlantic are reflected in regional differences in female body size and egg production responses, (5) differences in functional responses in egg production rate may reflect genetic differences between western and eastern populations, (6) dormancy duration is generally shorter in the deep waters adjacent to the lower latitude western North Atlantic shelves than in the east, and (7) differences in stage-specific mortality rates are related to bathymetry, temperature and potential predators, notably the abundance of congeners Calanus hyperboreus and C. glacialis, which likely feed on early life stages of C. finmarchicus. Two modeling approaches have previously been used to interpret the abundance and distribution of C. finmarchicus in relation to the North Atlantic habitat. A statistical approach based on ecological niche theory and a dynamical modeling approach, based on knowledge of spatial population dynamics and life history and implemented by recent developments in coupled physical-life cycle modeling. The strengths and weaknesses of each approach are discussed. A synthesis of the two modeling approaches to predict North Atlantic zooplankton species shifts, not only for C. finmarchicus, but also for other major taxa, is advocated. While the computational resource requirements and lack of species-specific life history information for physical-biological modeling hinder full application for many zooplankton taxa, use of the approach, where possible, to understand advective influences will provide insight for interpretation of statistical predictions from species distribution models.

Nature conservation and fisheries management often focus on particular seabed features that are considered vulnerable or important to commercial species. As a result, individual seabed types are protected in isolation, without any understanding of what effect the mixture of seabed types within the landscape has on ecosystem functions. Here we undertook predictive seabed modelling within a coastal marine protected area using observations from underwater stereo-video camera deployments and environmental information (depth, wave fetch, maximum tidal speeds, distance from coast and underlying geology). The effect of the predicted substratum type, extent and heterogeneity or the diversity of substrata, within a radius of 1500 m around each camera deployment of juvenile gadoid relative abundance was analysed. The predicted substratum model performed well with wave fetch and depth being the most influential predictor variables. Gadus morhua (Atlantic cod) were associated with relatively more rugose substrata (Algal-gravel-pebble and seagrass) and heterogeneous landscapes, than Melanogrammus aeglefinus (haddock) or Merlangius merlangus (whiting) (sand and mud). An increase in M. merlangus relative abundance was observed with increasing substratum extent. These results reveal that landscape effects should be considered when protecting the seabed for fish and not just individual seabed types. The landscape approach used in this study therefore has important implications for marine protected area, fisheries management and monitoring advice concerning demersal fish populations.

Fishing and other anthropogenic impacts have led to declines in many fish stocks and modification of the seabed. As a result, efforts to restore marine ecosystems have become increasingly focused on spatially explicit management methods to protect fish and the habitats they require for survival. This has led to a proliferation of investigations trying to map ‘habitats’ vulnerable to anthropogenic impacts and identify fish resource requirements in order to meet conservation and management needs. A wide range of habitat-related concepts, with different uses and understandings of the word ‘habitat’ itself has arisen as a consequence. Inconsistencies in terminology can cause confusion between studies, making it difficult to investigate and understand the ecology of fish and the factors that affect their survival. Ultimately, the inability to discern the relationships between fish and their environment clearly can hinder conservation and management measures for fish populations. This review identifies and addresses the present ambiguity surrounding definitions of ‘habitat’ and habitat-related concepts currently used in spatial management of demersal marine fish populations. The role of spatial and temporal scales is considered, in addition to examples of how to assess fish habitat for conservation and management purposes.

The North Atlantic copepods Calanus finmarchicus and C. helgolandicus are moving north in response to rising temperatures. Understanding the drivers of their relative geographic distributions is required in order to anticipate future changes. To explore this, we created a new spatially explicit stage-structured model of their populations throughout the North Atlantic. Recent advances in understanding Calanus biology, including U-shaped relationships between growth and fecundity and temperature, and a new model of diapause duration are incorporated in the model. Equations were identical for both species, but some parameters were species-specific. The model was parameterized using Continuous Plankton Recorder Survey data and tested using time series of abundance and fecundity. The geographic distributions of both species were reproduced by assuming that only known interspecific differences and a difference in the temperature influence on mortality exist. We show that differences in diapause capability are not necessary to explain why C. helgolandicus is restricted to the continental shelf. Smaller body size and higher overwinter temperatures likely make true diapause implausible for C. helgolandicus. Known differences were incapable of explaining why only C. helgolandicus exists southwest of the British Isles. Further, the fecundity of C. helgolandicus in the English Channel is much lower than we predict. We hypothesize that food quality is a key influence on the population dynamics of these species. The modelling framework presented can potentially be extended to further Calanus species.

Organic detritus entering, or produced, in the marine environment is re-mineralised to inorganic nutrient in the seafloor sediments. The flux of dissolved inorganic nutrient between the sediment and overlying water column is a key process in the marine ecosystem, which binds the biogeochemical sub-system to the living food web. These fluxes are potentially affected by a wide range of physical and biological factors and disentangling these is a significant challenge. Here we develop a set of General Additive Models (GAM) of nitrate, nitrite, ammonia, phosphate, silicate and oxygen fluxes, based on a year-long campaign of field measurements off the north-east coast of Scotland. We show that sediment grain size, turbidity due to sediment re-suspension, temperature, and biogenic matter content were the key factors affecting oxygen consumption, ammonia and silicate fluxes. However, phosphate fluxes were only related to suspended sediment concentrations, whilst nitrate fluxes showed no clear relationship to any of the expected drivers of change, probably due to the effects of denitrification. Our analyses show that the stoichiometry of nutrient regeneration in the ecosystem is not necessarily constant and may be affected by combinations of processes. We anticipate that our statistical modelling results will form the basis for testing the functionality of process-based mathematical models of whole-sediment biogeochemistry.

Spatial mapping of the marine environment is challenging when the properties concerned are difficult to measure except by shore-based analysis of discrete samples of material, usually from sparsely distributed sites. This is the case for many seabed sediment properties. We developed an indirect approach to mapping the organic content of coastal sediments from hydro-acoustic reflectance data. The basis was that both organic matter and acoustic reflectance are related to sediment type and grain size composition. Hence there is a collateral relationship between organic matter content and reflectance properties which can be exploited to enable high resolution mapping. We surveyed an area of seabed off the east coast of Scotland using a vessel mounted single beam echosounder with RoxAnn signal processing. Organic carbon, nitrogen and phytoplankton pigment contents were then measured in material from grab and core samples collected at intervals over a year. Relationships between the organic components and hydro–acoustic characteristics were derived by general additive models, and used to construct high resolution maps from the acoustic survey data. Our method is an advance on traditional interpolation techniques sparse spatial data, and represents a generic approach that could be applied to other properties.

Following the repeal in 1962 of a long-standing ban on trawling, yields of demersal fish from the Firth of Clyde, southwest Scotland, increased to a maximum in 1973 and then declined until the directed fishery effectively ceased in the early 2000s. Since then, the only landings of demersal fish from the Firth have been by-catch in the Norway lobster fishery. We analysed changes in biomass density, species diversity and length structure of the demersal fish community between 1927 and 2009 from scientific trawl surveys, and related these to the fishery harvesting rate. As yields collapsed, the community transformed from a state in which biomass was distributed across numerous species (high species evenness) and large maximum length taxa were common, to one in which 90 per cent of the biomass was vested in one species (whiting), and both large individuals and large maximum length species were rare. Species evenness recovered quickly once the directed fishery ceased, but 10 years later, the community was still deficient in large individuals. The changes partly reflected events at a larger regional scale but were more extreme. The lag in response with respect to fishing has implications for attempts at managing a restoration of the ecosystem.

This study focuses on a large region of the open ocean where we predict microzooplankton significantly influence foodweb structure over much of the year. The Irminger Sea exhibits low primary production that is generally poor for copepod production; in such waters ciliates and other microzooplankton can contribute significantly to the diets of holo- and mero- mesozooplankton and are major grazers of primary production. Surface plankton samples were collected during an extensive survey, across the basin and along one transect at several depths, over three seasons (winter, spring, summer), but not including the spring bloom. Microzooplankton and phytoplankton samples were fixed with Lugol’s solution and microscopically enumerated for species abundance; biomass was determined from cell volumes. Basin-scale distributions of abundance, biomass, and production were examined by geostatistical and multidimensional scaling methods. The dominance of the < 10 µm phytoplankton suggests that this should be a microzooplankton-dominated food web. Ciliates and heterotrophic dinoflagellates are abundant, in terms of numbers and biomass; heterotrophic dinoflagellates are more abundant than ciliates, but are less dominant in terms of biomass. Using ciliates as a proxy for all microzooplankton we suggest that there are seasonal patterns in occurrence, and there is no basin-scale patchiness related to hydrographic features. Through some simple, albeit “rough” calculations, we suggest that ciliate production may be sufficient to account for the removal of 15-30% of the < 10 µm primary production. If heterotrophic dinoflagellates were included in these estimates, they may be doubled (i.e. 30-60%). We, thus, contend that microzooplankton are major phytoplankton consumers in the system and should be carefully parameterised in models of this region.

In 1997 a monitoring site was established 5 km offshore from Stonehaven (56° 57.8′ N, 02° 06.2′ W) in the north east of Scotland to examine the effects of physical and chemical parameters on the plankton community in this region. Analysis of the first 10 years of data show that, in common with trends in the NE Atlantic, there was an increasing trend in temperature and salinity at the site. Nutrients were typical of unimpacted waters in this region, with nitrate being the main limiting nutrient over the summer months. The phytoplankton community composition showed strong seasonality with low phytoplankton biomass in the winter, diatoms dominating in spring and early summer and dinoflagellates appearing in mid to late summer. Two different regimes were recognised: from 1997–2000 and 2005–2006, where the chlorophyll concentration peaked in the early part of the year (mid month values ranging from 2.6–4.1 μg l− 1) and a period from 2001–2004 where chlorophyll mid month values did not exceed 2.5 μg l− 1. A decreasing trend in the abundance of dinoflagellates, including members of the genus Ceratium, was observed from 2003–2006. In addition, from 1997–2001, the diatom genus Chaetoceros was the dominant species in the spring bloom, but post 2001 Skeletonema spp. became more abundant. The study highlights the variability that exists in time series data and emphasises the need for long term time series to determine the long term trends and impacts of the phytoplankton community on the marine ecosystem.

Ecosystem-based management of the North Sea demersal fish community uses the large fish indicator (LFI), defined as the proportion by weight of fish caught in the International Bottom Trawl Survey (IBTS) exceeding a length of 40 cm. Current values of the LFI are ∼0.15, but the European Union (EU) Marine Strategy Framework Directive (MSFD) requires a value of 0.3 be reached by 2020. An LFI calculated from an eight-species subset correlated closely with the full community LFI, thereby permitting an exploration of the effects of various fishing scenarios on projected values of the LFI using an extension of a previously published multi-species length-structured model that included these key species. The model replicated historical changes in biomass and size composition of individual species, and generated an LFI that was significantly correlated with observations. A community-wide reduction in fishing mortality of ∼60% from 2008 values was necessary to meet the LFI target, driven mainly by changes in cod and saithe. A 70% reduction in cod fishing mortality alone, or a 75% reduction in otter trawl effort, was also sufficient to achieve the target. Reductions in fishing mortality necessary to achieve maximum sustainable harvesting rates are projected to result in the LFI over-shooting its target.