An individual-based model of the early life history of mackerel (Scomber scombrus) in the eastern North Atlantic, simulating transport, growth and mortality

The main purpose of this paper is to provide the core description of the modelling exercise within the Shelf Edge Advection Mortality And Recruitment (SEAMAR) programme. An individual-based model (IBM) was developed for the prediction of year-to-year survival of the early life-history stages of mackerel (Scomber scombrus) in the eastern North Atlantic. The IBM is one of two components of the model system. The first component is a circulation model to provide physical input data for the IBM. The circulation model is a geographical variant of the HAMburg Shelf Ocean Model (HAMSOM). The second component is the IBM, which is an i-space configuration model in which large numbers of individuals are followed as discrete entities to simulate the transport, growth and mortality of mackerel eggs, larvae and post-larvae. Larval and post-larval growth is modelled as a function of length, temperature and food distribution; mortality is modelled as a function of length and absolute growth rate. Each particle is considered as a super-individual representing 10 super(6) eggs at the outset of the simulation, and then declining according to the mortality function. Simulations were carried out for the years 1998-2000. Results showed concentrations of particles at Porcupine Bank and the adjacent Irish shelf, along the Celtic Sea shelf-edge, and in the southern Bay of Biscay. High survival was observed only at Porcupine and the adjacent shelf areas, and, more patchily, around the coastal margin of Biscay. The low survival along the shelf-edge of the Celtic Sea was due to the consistently low estimates of food availability in that area.

Reduced pH sea water disrupts chemo-responsive behaviour in an intertidal crustacean

Chemoreception is a key activity by which many aquatic animals perceive their environment, and therefore abiotic disruptions to this process could have serious impacts on the survival and fitness of individuals, and on species interactions. Hermit crabs are subject to cyclical reductions in the pH of the water in the intertidal rock pools that they inhabit. Such reductions may be further exacerbated by ongoing ocean acidification and/or leakage of carbon dioxide from geological storage sites and coastal upwelling events. Here we test the chemo-sensory responses of the hermit crab Pagurus bernhardus (Linnaeus) to a food odour under reduced pH conditions (pHNBS = 6.80). Acidifying the odour had no effect on its attractiveness indicating no permanent degradation of the cue; however, the pH of the sea water did affect the crabs' responses. Hermit crabs kept and tested in reduced pH sea water had lower antennular flicking rates (the ‘sniffing’ response in decapods); were less successful in locating the odour source, and showed an overall decline in locomotory activity compared to those in untreated sea water. Analysis of their haemolymph revealed a greater concentration of chloride ions ([Cl−]) in the reduced pH treatment group, suggesting iono-regulatory disruption; however, there was no correlation between [Cl−] and locomotory activity, suggesting a specific effect on chemoreception. This study shows that the chemo-responsiveness of a crustacean may be influenced by both naturally occurring pH fluctuations and future anthropogenically-induced changes in ocean pH.

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms

The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms with pCO(2) levels ranging from similar to 145 to similar to 1420 mu atm. Samples for the present study were collected at ten time points (t-1, t1, t5, t7, t12, t14, t18, t22, t26 to t28) in seven treatments (ambient fjord (similar to 145), 2x similar to 185, similar to 270, similar to 685, similar to 820, similar to 1050 mu atm) and were analysed for "small" and "large" size fraction microbial community composition using 16S rRNA (ribosomal ribonucleic acid) amplicon sequencing. This high-throughput sequencing analysis produced similar to 20 000 000 16S rRNA V4 reads, which comprised 7000OTUs. The main variables structuring these communities were sample origins (fjord or mesocosms) and the community size fraction (small or large size fraction). The community was significantly different between the unenclosed fjord water and enclosed mesocosms (both control and elevated CO2 treatments) after nutrients were added to the mesocosms, suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The sampling strategy of separating the small and large size fraction was the second most important factor for community structure. When the small and large size fraction bacteria were analysed separately at different time points, the only taxon pCO(2) was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO(2) treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.

Measurements of OVOC fluxes by eddy covariance using a proton-transfer-reaction mass spectrometer – method development at a coastal site

We present here vertical fluxes of oxygenated volatile organic compounds (OVOCs) measured with eddy covariance (EC) during the period of March to July 2012 near the southwest coast of the United Kingdom. The performance of the proton-transfer-reaction mass spectrometer (PTR-MS) for flux measurement is characterized, with additional considerations given to the homogeneity and stationarity assumptions required by EC. Observed mixing ratios and fluxes of OVOCs (specifically methanol, acetaldehyde, and acetone) vary significantly with time of day and wind direction. Higher mixing ratios and fluxes of acetaldehyde and acetone are found in the daytime and from the direction of a forested park, most likely due to light-driven emissions from terrestrial plants. Methanol mixing ratio and flux do not demonstrate consistent diel variability, suggesting sources in addition to plants. We estimate air-sea exchange and photochemical rates of these compounds, which are compared to measured vertical fluxes. For acetaldehyde, the mean (1 sigma) mixing ratio of 0.13 (0.02) ppb at night may be maintained by oceanic emission, while photochemical destruction out-paces production during the day. Air-sea exchange and photochemistry are probably net sinks of methanol and acetone in this region. Their nighttime mixing ratios of 0.46 (0.20) and 0.39 (0.08) ppb appear to be affected more by terrestrial emissions and long-distance transport, respectively.

Covariance among North Sea ecosystem state indicators during the past 50 years - contrasts between coastal and open waters

Regime shift and principal component analysis of a spatially disaggregated database capturing time-series of climatic, nutrient and plankton variables in the North Sea revealed considerable covariance between groups of ecosystem indicators. Plankton and climate time-series span the period 1958–2003, those of nutrients start in 1980. In both regions, the period from 1989 to 2001 identified in principal component 1 had warmer surface waters, higher Atlantic inflow and stronger winds, than the periods before or after. However, it was preceded by a regime shift in both open (PC2) and coastal (PC3) waters during 1977 towards more hours of sunlight and higher water temperature, which lasted until 1997. The relative influence of nutrient availability and climatic forcing differed between open and coastal North Sea regions. Inter-annual variability in phytoplankton dynamics of the open North Sea was primarily regulated by climatic forcing, specifically by sea surface temperature, Atlantic inflow and co-varying wind stress and NAO. Coastal phytoplankton variability, however, was regulated by insolation and sea surface temperature, as well as Si availability, but not by N or P. Regime shifts in principal components of hydrographic and climatic variables (explaining 55 and 61% of the variance in coastal and open water variables) were detected using Rodionov's sequential t-test. These shifts in hydroclimatic variables which occurred around 1977, 1989, 1997 and 2001, were synchronized in open and coastal waters, and were tracked by open water chlorophyll and copepods, but not by coastal plankton. North–central–south or open-coastal spatial breakdowns of the North Sea explained similar amounts of variability in most ecosystem indicators with the exception of diatom abundance and chlorophyll concentration, which were clearly better explained using the open-coastal configuration.

ALES: a multi-mission adaptive sub-waveform retracker for coastal and open ocean altimetry

Satellite altimetry has revolutionized our understanding of ocean dynamics thanks to frequent sampling and global coverage. Nevertheless, coastal data have been flagged as unreliable due to land and calm water interference in the altimeter and radiometer footprint and uncertainty in the modelling of high-frequency tidal and atmospheric forcing. Our study addresses the first issue, i.e. altimeter footprint contamination, via retracking, presenting ALES, the Adaptive Leading Edge Subwaveform retracker. ALES is potentially applicable to all the pulse-limited altimetry missions and its aim is to retrack both open ocean and coastal data with the same accuracy using just one algorithm. ALES selects part of each returned echo and models it with a classic ”open ocean” Brown functional form, by means of least square estimation whose convergence is found through the Nelder-Mead nonlinear optimization technique. By avoiding echoes from bright targets along the trailing edge, it is capable of retrieving more coastal waveforms than the standard processing. By adapting the width of the estimation window according to the significant wave height, it aims at maintaining the accuracy of the standard processing in both the open ocean and the coastal strip. This innovative retracker is validated against tide gauges in the Adriatic Sea and in the Greater Agulhas System for three different missions: Envisat, Jason-1 and Jason-2. Considerations of noise and biases provide a further verification of the strategy. The results show that ALES is able to provide more reliable 20-Hz data for all three missions in areas where even 1-Hz averages are flagged as unreliable in standard products. Application of the ALES retracker led to roughly a half of the analysed tracks showing a marked improvement in correlation with the tide gauge records, with the rms difference being reduced by a factor of 1.5 for Jason-1 and Jason-2 and over 4 for Envisat in the Adriatic Sea (at the closest point to the tide gauge).

The dispersal of phytoplankton populations by enhanced turbulent mixing in a shallow coastal sea

A single tidal cycle survey in a Lagrangian reference frame was conducted in autumn 2010 to evaluate the impact of short-term, episodic and enhanced turbulent mixing on large chain-forming phytoplankton. Observations of turbulence using a free-falling microstructure profiler were undertaken, along with near-simultaneous profiles with an in-line digital holographic camera at station L4 (50° 15′ N 4° 13′ W, depth 50 m) in the Western English Channel. Profiles from each instrument were collected hourly whilst following a drogued drifter. Results from an ADCP attached to the drifter showed pronounced vertical shear, indicating that the water column structure consisted of two layers, restricting interpretation of the Lagrangian experiment to the upper ~ 25 m. Atmospheric conditions deteriorated during the mid-point of the survey, resulting in values of turbulent dissipation reaching a maximum of 10− 4 W kg− 1 toward the surface in the upper 10 m. Chain-forming phytoplankton > 200 μm were counted using the data from the holographic camera for the two periods, before and after the enhanced mixing event. As mixing increased phytoplankton underwent chain breakage, were dispersed by advection through their removal from the upper to lower layer and subjected to aggregation with other suspended material. Depth averaged counts of phytoplankton were reduced from a maximum of around 2050 L− 1 before the increased turbulence, to 1070 L− 1 after, with each of these mechanisms contributing to this reduction. These results demonstrate the sensitivity of phytoplantkon populations to moderate increases in turbulent activity, yielding consequences for accurate forecasting of the role played by phytoplankton in climate studies and also for the ecosystem in general in their role as primary producers.

Scenarios for integrated river catchment and coastal zone management

The European Water Framework Directive requires EU Member States to introduce water quality objectives for all water bodies, including coastal waters. Measures will have to be introduced if these objectives are not met, given predictions based on current trends. In this context, the estimation of future fluxes of nutrients and contaminants in the catchment, and the evaluation of policies to improve water quality in coastal zones are an essential part of river basin management plans. This paper investigates the use of scenarios for integrated catchment/coastal zone management in the Humber Estuary in the U.K. The context of this ongoing research is a European research project which aims to assist the implementation of integrated catchment and coastal zone management by analysing the response of the coastal sea to changes in fluxes of nutrients and contaminants from the catchments. The example of the Humber illustrates how scenarios focusing on water quality improvement can provide a useful tool to investigate future fluxes and evaluate policy options for a more integrated coastal/catchment management strategy.

Ecohydrodynamics of cold-water coral reefs: A case study of the Mingulay Reef complex (western Scotland)

Ecohydrodynamics investigates the hydrodynamic constraints on ecosystems across different temporal and spatial scales. Ecohydrodynamics play a pivotal role in the structure and functioning of marine ecosystems, however the lack of integrated complex flow models for deep-water ecosystems beyond the coastal zone prevents further synthesis in these settings. We present a hydrodynamic model for one of Earth's most biologically diverse deep-water ecosystems, cold-water coral reefs. The Mingulay Reef Complex (western Scotland) is an inshore seascape of cold-water coral reefs formed by the scleractinian coral Lophelia pertusa. We applied single-image edge detection and composite front maps using satellite remote sensing, to detect oceanographic fronts and peaks of chlorophyll a values that likely affect food supply to corals and other suspension-feeding fauna. We also present a high resolution 3D ocean model to incorporate salient aspects of the regional and local oceanography. Model validation using in situ current speed, direction and sea elevation data confirmed the model's realistic representation of spatial and temporal aspects of circulation at the reef complex including a tidally driven current regime, eddies, and downwelling phenomena. This novel combination of 3D hydrodynamic modelling and remote sensing in deep-water ecosystems improves our understanding of the temporal and spatial scales of ecological processes occurring in marine systems. The modelled information has been integrated into a 3D GIS, providing a user interface for visualization and interrogation of results that allows wider ecological application of the model and that can provide valuable input for marine biodiversity and conservation applications.

Satellite discrimination of Karenia mikimotoi and Phaeocystis harmful algal blooms in European coastal waters: Merged classification of ocean colour data

The detection of dense harmful algal blooms (HABs) by satellite remote sensing is usually based on analysis of chlorophyll-a as a proxy. However, this approach does not provide information about the potential harm of bloom, nor can it identify the dominant species. The developed HAB risk classification method employs a fully automatic data-driven approach to identify key characteristics of water leaving radiances and derived quantities, and to classify pixels into “harmful”, “non-harmful” and “no bloom” categories using Linear Discriminant Analysis (LDA). Discrimination accuracy is increased through the use of spectral ratios of water leaving radiances, absorption and backscattering. To reduce the false alarm rate the data that cannot be reliably classified are automatically labelled as “unknown”. This method can be trained on different HAB species or extended to new sensors and then applied to generate independent HAB risk maps; these can be fused with other sensors to fill gaps or improve spatial or temporal resolution. The HAB discrimination technique has obtained accurate results on MODIS and MERIS data, correctly identifying 89% of Phaeocystis globosa HABs in the southern North Sea and 88% of Karenia mikimotoi blooms in the Western English Channel. A linear transformation of the ocean colour discriminants is used to estimate harmful cell counts, demonstrating greater accuracy than if based on chlorophyll-a; this will facilitate its integration into a HAB early warning system operating in the southern North Sea.