The carbonate system of the NW European shelf: sensitivity and model validation

The ocean plays an important role in regulating the climate, acting as a sink for carbon dioxide, perturbing the carbonate system and resulting in a slow decrease of seawater pH. Understanding the dynamics of the carbonate system in shelf sea regions is necessary to evaluate the impact of Ocean Acidification (OA) in these societally important ecosystems. Complex hydrodynamic and ecosystem coupled models provide a method of capturing the significant heterogeneity of these areas. However rigorous validation is essential to properly assess the reliability of such models. The coupled model POLCOMS–ERSEM has been implemented in the North Western European shelf with a new parameterization for alkalinity explicitly accounting for riverine inputs and the influence of biological processes. The model has been validated in a like with like comparison with North Sea data from the CANOBA dataset. The model shows good to reasonable agreement for the principal variables, physical (temperature and salinity), biogeochemical (nutrients) and carbonate system (dissolved inorganic carbon and total alkalinity), but simulation of the derived variables, pH and pCO2, are not yet fully satisfactory. This high uncertainty is attributed mostly to riverine forcing and primary production. This study suggests that the model is a useful tool to provide information on Ocean Acidification scenarios, but uncertainty on pH and pCO2 needs to be reduced, particularly when impacts of OA on ecosystem functions are included in the model systems.

The assessment of a global marine ecosystem model on the basis of emergent properties and ecosystem function: a case study with ERSEM

Ecosystem models are often assessed using quantitative metrics of absolute ecosystem state, but these model-data comparisons are disproportionately vulnerable to discrepancies in the location of important circulation features. An alternative method is to demonstrate the models capacity to represent ecosystem function; the emergence of a coherent natural relationship in a simulation indicates that the model may have an appropriate representation of the ecosystem functions that lead to the emergent relationship. Furthermore, as emergent properties are large-scale properties of the system, model validation with emergent properties is possible even when there is very little or no appropriate data for the region under study, or when the hydrodynamic component of the model differs significantly from that observed in nature at the same location and time. A selection of published meta-analyses are used to establish the validity of a complex marine ecosystem model and to demonstrate the power of validation with emergent properties. These relationships include the phytoplankton community structure, the ratio of carbon to chlorophyll in phytoplankton and particulate organic matter, the ratio of particulate organic carbon to particulate organic nitrogen and the stoichiometric balance of the ecosystem. These metrics can also inform aspects of the marine ecosystem model not available from traditional quantitative and qualitative methods. For instance, these emergent properties can be used to validate the design decisions of the model, such as the range of phytoplankton functional types and their behaviour, the stoichiometric flexibility with regards to each nutrient, and the choice of fixed or variable carbon to nitrogen ratios.

Technical Note: Ensuring consistent, global measurements of short-lived halocarbon gases in the ocean and atmosphere

Very short-lived halocarbons are significant sources of reactive halogen in the marine boundary layer, and likely in the upper troposphere and lower stratosphere. Quantifying ambient concentrations in the surface ocean and atmosphere is essential for understanding the atmospheric impact of these trace gas fluxes. Despite the body of literature increasing substantially over recent years, calibration issues complicate the comparison of results and limit the utility of building larger-scale databases that would enable further development of the science (e.g. sea-air flux quantification, model validation, etc.). With this in mind, thirty-one scientists from both atmospheric and oceanic halocarbon communities in eight nations gathered in London in February 2008 to discuss the scientific issues and plan an international effort toward developing common calibration scales (http://tinyurl.com/c9cg58). Here, we discuss the outputs from this meeting, suggest the compounds that should be targeted initially, identify opportunities for beginning calibration and comparison efforts, and make recommendations for ways to improve the comparability of previous and future measurements.

Strong links between phytoplankton community physiology and dimethylsulphoniopropionate (DMSP) concentrations in the sub-tropical/tropical Atlantic

We present an extensive dataset of dimethylsulphide (DMS, n = 651) and dimethylsulphoniopropionate (DMSP, n = 590) from the Atlantic Meridional Transect programme. These data are used to derive representative depth profiles that illustrate observed natural variations and can be used for DMS and DMSP model-validation in oligotrophic waters. To further understand our dataset, we interpret the data with a wide range of accompanying parameters that characterise the prevailing biogeochemical conditions and phytoplankton community physiology, activity, taxonomic composition, and capacity to cope with light stress. No correlations were observed with typical biomarker pigments for DMSP-producing species. However, strong correlations were found between DMSP and primary production by cells >2 µm in diameter, and between DMSP and some photo-protective pigments. These parameters are measures of mixed phytoplankton communities, so we infer that such associations are likely to be stronger in DMSP-producing organisms. Further work is warranted to develop links between community parameters, DMS and DMSP at the global scale.

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.

Decadal reanalysis of biogeochemical indicators and fluxes in the North West European shelf-sea ecosystem

In this paper we present the first decadal reanalysis simulation of the biogeochemistry of the North West European shelf, along with a full evaluation of its skill and value. An error-characterized satellite product for chlorophyll was assimilated into a physical-biogeochemical model of the North East Atlantic, applying a localized Ensemble Kalman filter. The results showed that the reanalysis improved the model predictions of assimilated chlorophyll in 60% of the study region. Model validation metrics showed that the reanalysis had skill in matching a large dataset of in situ observations for ten ecosystem variables. Spearman rank correlations were significant and higher than 0.7 for physical-chemical variables (temperature, salinity, oxygen), ∼0.6 for chlorophyll and nutrients (phosphate, nitrate, silicate), and significant, though lower in value, for partial pressure of dissolved carbon dioxide (∼0.4). The reanalysis captured the magnitude of pH and ammonia observations, but not their variability. The value of the reanalysis for assessing environmental status and variability has been exemplified in two case studies. The first shows that between 340,000-380,000 km2 of shelf bottom waters were oxygen deficient potentially threatening bottom fishes and benthos. The second application confirmed that the shelf is a net sink of atmospheric carbon dioxide, but the total amount of uptake varies between 36-46 Tg C yr−1 at a 90% confidence level. These results indicate that the reanalysis output dataset can inform the management of the North West European shelf ecosystem, in relation to eutrophication, fishery, and variability of the carbon cycle.

Validation of the NEMO-ERSEM operational ecosystem model for the North West European Continental Shelf

This paper details updates to the Met Office's operational coupled hydrodynamic-ecosystem model from the 7 km Medium-Resolution Continental Shelf – POLCOMS-ERSEM (MRCS-PE) system (Siddorn et al., 2007) to the 7 km Atlantic Margin Model NEMO-ERSEM (AMM7-NE) system. We also provide a validation of the ecosystem component of the new operational system. Comparisons have been made between the model variables and available in situ, satellite and climatological data. The AMM7-NE system has also been benchmarked against the MRCS-PE system. The transition to the new AMM7-NE system was successful and it has been running operationally since March 2012 and has been providing products through MyOcean (http://www.myocean.eu.org) since that time. The results presented herein show the AMM7-NE system performs better than the MRCS-PE system with the most improvement in the model nutrient fields. The problem of nutrient accumulation in the MRCS-PE system appears to be solved in the new AMM7-NE system with nutrient fields improved throughout the domain as discussed in Sect. 4. Improvements in model chlorophyll are also seen but are more modest.

ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The ERSEM model is one of the most established ecosystem models for the lower trophic levels of the marine food-web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North-Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic part of the marine ecosystem, including the microbial food-web, the carbonate system and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case-studies of mesocosm type simulations, water column implementations and a brief example of a full-scale application for the North-West European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The European Regional Seas Ecosystem Model (ERSEM) is one of the most established ecosystem models for the lower trophic levels of the marine food web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic parts of the marine ecosystem, including the microbial food web, the carbonate system, and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case studies of mesocosm-type simulations, water column implementations, and a brief example of a full-scale application for the north-western European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.