BGC-val: a model- and grid-independent Python toolkit to evaluate marine biogeochemical models

The biogeochemical evaluation toolkit, BGC-val, is a model- and grid-independent Python toolkit that has been built to evaluate marine biogeochemical models using a simple interface. Here, we present the ideas that motivated the development of the BGC-val software framework, introduce the code structure, and show some applications of the toolkit using model results from the Fifth Climate Model Intercomparison Project (CMIP5). A brief outline of how to access and install the repository is presented in Appendix A, but the specific details on how to use the toolkit are kept in the code repository. The key ideas that directed the toolkit design were model and grid independence, front-loading analysis functions and regional masking, interruptibility, and ease of use. We present each of these goals, why they were important, and what we did to address them. We also present an outline of the code structure of the toolkit illustrated with example plots produced by the toolkit. After describing BGC-val, we use the toolkit to investigate the performance of the marine physical and biogeochemical quantities of the CMIP5 models and highlight some predictions about the future state of the marine ecosystem under a business-as-usual CO2 concentration scenario (RCP8.5)

Acclimation, Adaptation, Traits and Trade-Offs in Plankton Functional Type Models: Reconciling Terminology for Biology and Modelling

We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism functional type should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology is also consistent with usage in terrestrial science. Adaptation should be confined, as in genetics, to consideration of species inter-generational change; most so-called adaptive plankton models are thus acclimative, modifying vital rates in response to stimuli. Trait trade-off approaches should ideally only be considered for describing intra-generational interactions; in applications between generations, and certainly between unrelated species, such concepts should be avoided. We suggest that systems biology approaches, through to complex adaptive/acclimative systems modelling, with explicit modelling of feedback processes (which we suggest should define mechanistic models), would provide realistic and flexible bases upon which to develop descriptions of functional type models

Marine regime shifts in ocean biogeochemical models:a case study in the Gulf of Alaska

Regime shifts have been reported in many marine ecosystems, and are often expressed as an abrupt change occurring in multiple physical and biological components of the system. In the Gulf of Alaska, a regime shift in the late 1970s was observed, indicated by an abrupt increase in sea surface temperature and major shifts in the catch of many fish species. A thorough understanding of the extent and mechanisms leading to such regime shifts is challenged by data paucity in time and space. We investigate the ability of a suite of ocean biogeochemistry models of varying complexity to simulate regime shifts in the Gulf of Alaska by examining the presence of abrupt changes in time series of physical variables (sea surface temperature and mixed-layer depth), nutrients and biological variables (chlorophyll, primary productivity and plankton biomass) using change-point analysis. Our results show that some ocean biogeochemical models are capable of simulating the late 1970s shift, manifested as an abrupt increase in sea surface temperature followed by an abrupt decrease in nutrients and biological productivity. Models from low to intermediate complexity simulate an abrupt transition in the late 1970s (i.e. a significant shift from one year to the next) while the transition is smoother in higher complexity models. Our study demonstrates that ocean biogeochemical models can successfully simulate regime shifts in the Gulf of Alaska region. These models can therefore be considered useful tools to enhance our understanding of how changes in physical conditions are propagated from lower to upper trophic levels

Challenges in integrative approaches to modelling the marine ecosystems of the North Atlantic: Physics to Fish and Coasts to Ocean

It has long been recognized that there are strong interactions and feedbacks between climate, upper ocean biogeochemistry and marine food webs, and also that food web structure and phytoplankton community distribution are important determinants of variability in carbon production and export from the euphotic zone. Numerical models provide a vital tool to explore these interactions, given their capability to investigate multiple connected components of the system and the sensitivity to multiple drivers, including potential future conditions. A major driver for ecosystem model development is the demand for quantitative tools to support ecosystem-based management initiatives. The purpose of this paper is to review approaches to the modelling of marine ecosystems with a focus on the North Atlantic Ocean and its adjacent shelf seas, and to highlight the challenges they face and suggest ways forward. We consider the state of the art in simulating oceans and shelf sea physics, planktonic and higher trophic level ecosystems, and look towards building an integrative approach with these existing tools. We note how the different approaches have evolved historically and that many of the previous obstacles to harmonisation may no longer be present. We illustrate this with examples from the on-going and planned modelling effort in the Integrative Modelling work package of the EURO-BASIN programme

Biological or microbial carbon pump? The role of phytoplankton stoichiometry in ocean carbon sequestration

Once fixed by photosynthesis carbon becomes part of the marine food web. The fate of this carbon has two possible outcomes: it may be respired and released back to the ocean and potentially to the atmosphere as CO2 or retained in the ocean interior and/or marine sediments for extended time scales. The most important biologically mediated processes responsible for long term carbon storage in the ocean are the biological carbon pump (BCP) and the microbial carbon pump (MCP). While acting simultaneously in the ocean, the balance between these two mechanisms is thought to vary depending on the trophic state of the environment. Using previously published formulations, we propose a modelling framework to simulate variability in the MCP: BCP ratio as a function of external nutrients. Our results suggest that the role of the MCP might become more significant under future climate change conditions where increased stratification enhances the oligotrophic nature of the surface ocean. Based on these model results, we propose a conceptual framework in which the internal stoichiometry of phytoplankton, modulating both grazing pressure and DOM production (via phytoplankton exudation), plays a crucial role in regulating the MCP: BCP ratio

Unstructured grid modelling of offshore wind farm impacts on seasonally stratified shelf seas

Shelf seas comprise approximately 7% of the world’s oceans and host enormous economic activity. Development of energy installations (e.g. Offshore Wind Farms (OWFs), tidal turbines) in response to increased demand for renewable energy requires a careful analysis of potential impacts. Recent remote sensing observations have identified kilometrescale impacts from OWFs. Existing modelling evaluating monopile impacts has fallen into two camps: small-scale models with individually resolved turbines looking at local effects; and large-scale analyses but with sub-grid scale turbine parameterisations. This work straddles both scales through a 3D unstructured grid model (FVCOM): wind turbine monopiles in the eastern Irish Sea are explicitly described in the grid whilst the overall grid domain covers the south-western UK shelf. Localised regions of decreased velocity extend up to 250 times the monopile diameter away from the monopile. Shelf-wide, the amplitude of the M2 tidal constituent increases by up to 7%. The turbines enhance localised vertical mixing which decreases seasonal stratification. The spatial extent of this extends well beyond the turbines into the surrounding seas. With significant expansion of OWFs on continental shelves, this work highlights the importance of how OWFs may impact coastal (e.g. increased flooding risk) and offshore (e.g. stratification and nutrient cycling) areas

How well can we forecast high biomass algal bloom events in a eutrophic coastal sea?

High biomass algal bloom events are a characteristic of eutrophic coastal waters; these may result both in ecosystem degradation and economic loss. We present a skill evaluation of a coupled hydrodynamic ecosystem model of the NW European shelf for predicting bloom events based on a comparison with satellite chlorophyll estimates. By setting thresholds to define bloom events we use a binary classification system to generate maps showing the probability a model bloom prediction is correct. Model and satellite data limitations are discussed along with the application of this method to forecasting specific harmful algal species

Modeling of nutrient dynamics in a coastal lagoon through ecosystem model

San Quintin Bay (SQB), Baja California (30º27’N-116º00’W), is a shallow (~ 2 m depth average) hypersaline coastal lagoon strongly influenced by upwelling events in Spring and Summer. Upwelling events and tidal pumping are the main cause of temporal variability of biological and chemical parameters throughout the lagoon. In order to describe nutrient and primary producer biomass dynamics, the European Regional Seas Ecosystem Model (ERSEM) was coupled with the 1-D physical General Ocean Turbulence Model (GOTM). ERSEM, an ecosystem-model originally developed for shelf waters, was adapted to SQB conditions by adding seagrass (Zostera marina) and macroalgae (Ulva spp.) modules in a way conceptually similar to that employed in ERSEM for pelagic phytoplankton and microphytobenthos. Sensitivity analyses are allowing the adjustment of key parameters to reproduce the seasonal dynamics of primary producer biomass, as the supply of nitrate apparently determine the seasonality of Ulva and phytoplankton that reach their maxima during the upwelling season. The maximum seagrass biomass occurs in late summer (non or weak upwelling) and its productivity depends on recycled nitrogen but is mostly controlled by light availabilit

A highly spatially resolved ecosystem model for the North West European Continental Shelf

This paper outlines an approach to complex spatio-temporal marine ecosystem modelling as applied to the North Western European Continental Shelf. The model presented here goes further than previous work, as we combine a higher resolution hydrodynamic model, the POL-3DB baroclinic model with the European Regional Seas Ecosystem Model. This combination of models includes many of the processes (benthic-pelagic coupling, dynamic zooplankton and nitrogen, phosphorous and silicate cycling) previous authors have identitied as missing from their models and partially responsible for the inadequacies of their simulations. Spatial distributions of key physical and ecological variables taken from the three dimensional high resolution hydrodynamic/ecological simulations are presented to illustrate how spatial and temporal variations in physical processes determine the onset of the spring bloom in the North Sea. A basic validation of these simulations is presented, which indicates the model reproduces many of the features of the seasonal cycles of nutrients and phytoplankton, but fails to simulate mesozooplankton biomass in a convincing manner. The reasons for this are discussed along with potential new research directions