Integrated Marine Biogeochemical Modelling Network to Support UK Earth System Research

Lead Research Organisation: Plymouth Marine Laboratory
Department Name: Plymouth Marine Lab


Biogeochemistry is the study of the cycles of chemical elements, such as carbon and nitrogen, which are either driven by or have an impact on biological activity. The biogeochemistry of the oceans plays an important role in the Earth System: it regulates the cycles of major chemical elements and controls the associated feedback processes between the land, ocean and atmosphere. The oceans currently take up about 25% of the carbon dioxide emitted by human activities, storing it in deep waters for centuries. This uptake occurs against the backdrop of an active natural carbon cycle, where carbon is constantly recirculated between the surface and deep ocean in response to physical, chemical and biological processes. As a result, changes to ocean biology can influence the uptake of carbon dioxide by the oceans, and can have important implications for climate. While the physical and chemical processes that affect ocean biogeochemical cycles are relatively well understood (e.g. circulation, solubility), our understanding of the role of biological processes is far less advanced. In large part this stems from the complexity of elemental cycling within living organisms, and the high diversity (taxonomic and functional) of marine communities. At present, marine ecosystems are affected by anthropogenic environmental change particularly through climate-induced changes in physical properties (e.g. ocean currents and temperature) and by ocean acidification (e.g. carbon dioxide-mediated drop in pH). If we are to maintain a safe environment in this century and beyond it is essential that we improve our understanding of ocean biogeochemistry so that we can better forecast and quantify its response to global change, and so that we can better identify potential feedbacks between the ocean and the rest of the Earth System.

By synthesising empirical knowledge into quantitative descriptions, computer models allow scientists to investigate the functioning of, and interactions between, biogeochemistry and climate. Earth Systems models now routinely simulate the biogeochemical interactions of the biosphere, atmosphere, oceans, land surface, and cryosphere in order to study the dynamics of the climate system and to make projections of future climate. A joint goal of NERC and the UK Met. Office is to develop a new earth system model capable of predicting global and regional impacts of environmental change from days to decades. This will include a novel and unified biological modelling approach for ocean biogeochemistry. The detail required to adequately represent the ocean biogeochemical processes relevant to climate in a numerical model is a subject of much ongoing debate. This has led to a diversity of models which differ not only in their structure, but also in their formulation and parameterisation of key biological processes.

i-MarNet will evaluate the existing suite of ocean biogeochemical models in the UK in order to inform the decision for the next UK earth system model. Simulations of both the recent past and the next 100 years will be made to assess the ability of models to reproduce observations and to quantify the change and responsiveness of the models to climate change. This model comparison will provide new information that helps to identify the role of ecosystem complexity in the representation of biological activity and the ocean carbon dioxide sink, as well as the of both sensitivity to climate change. i-MarNet will also generate a strategic plan, via coordination of the UK science community, to develop a new state of the art ocean biogeochemical model that builds on the best available science and the strength of existing models.

In summary, the project will provide crucial information to guide ocean biogeochemical model developments in the UK, and will define a roadmap to help resolve key scientific questions as well as provide a better understanding of the functioning of the climate system that improves climate projections

Planned Impact

Impact Summary
Who will benefit from this research?

Department of Energy and Climate Change (DECC)
Department of Environment Food and Rural Affairs (Defra)
Ministry of Defence (MoD)
EU member states

The international climate evidence community (embodied by the IPCC)
Met. Office Hadley Centre
National Centre for Ocean Forecasting (NCOF)
Marine Climate Change Impacts Partnership (MCCIP)
Marine Management Organisation (MMO)

Wider public:
UK and international general public

How will they benefit from this research?

DECC and the international climate community (embodied by the IPCC) will benefit through our rigorous investigation and evaluation of the UK's existing ocean biogeochemical models in the NEMO ocean model. This will take place through engagement with the UK Met Office (UKMO), continuing a close working relationship and the use of a common ocean model, NEMO. This will provide the ocean biogeochemical component for the next generation of coupled climate models at UKMO. These impacts will be reinforced thought engagement with the international MAREMIP and RECCAP projects through the Global Carbon Project UK office at UEA Tyndall Centre.

In addressing productivity at the lower trophic levels of the marine food web, including forecasting it to century-scale, our research may assist the development of marine fisheries policy and approaches for working towards an ecosystem-focused approach to marine resource management.

Wider public
We will publicise our research through:

A project website
Engagement with the media as appropriate


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Anderson T (2015) EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R in Geoscientific Model Development

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Flynn KJ (2020) Exploring evolution of maximum growth rates in plankton. in Journal of plankton research

Description i-MarNet aimed to provide a framework and pathway for the development of a new biogeochemical model/model hierarchy for use by the UK science community.

The project has undertaken the evaluation of the performance of marine biogeochemical models of differing complexity via a coordinated model inter-comparison and the development and use of robust, process-based model metrics.

Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry - climate interactions.

A report has been prepared to analyse candidate ocean biogeochemical models and provide the UK Hadley Centre with the information required to make an informed decision regarding ocean biogeochemical model implementation in the next UK Earth System Model (UKESM1). The report seeks to asses any potential trade-offs between ocean biogeochemical model complexities, model efficacies in an Earth System context, and computational cost. This work has helped inform the selection of MEDUSA is the baseline OBM for the next UK ESM.

We investigated 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.
Exploitation Route I-Marnet provide a valuable framework for the assessment of the suitability of ocean biogeochemistry models for inclusions in ESM's. Models have been assessed in terms of:

Biological fidelity: structures, parameterisations and parameter sets of candidate models have been expertly assessed in a network workshop with a view to their realism and use of "best practise".

Computational cost: in consultation with the UK Met Office each candidate model has been benchmarked for its computational cost and data storage requirements.

Model skill: in consultation with model developers a set of common ocean biogeochemical model outputs have been assessed against observational datasets. Model skill has been assessed through traditional "beauty contest" statistical techniques that take into account mean model biases and spatial pattern correlation coefficients. Although this analysis forms the bulk of this report we also explore "emergent constraints" as an innovative method of assessing model skill with respect to climate projections which makes optimal use of an ensemble of ocean biogeochemical models.

The recommendation was the adoption of Medusa-2 as the OBGC component of UKESM1. _ More generally, the very constructive iMarNet collaboration offers a promising basis for the UK to take the lead in developing the more complex ocean ecosystem models capable of addressing broader issues of environmental change, beyond the representation of biogeochemical feedbacks in Earth System Models.
Sectors Environment

Description The findings of the project have been use to help select the ocean biogeochemistry component of UKESM1. UKESM1 is being developed jointly by NERC and the UKMO as a simulation tool for the UK participation in CMIP6 and the next IPCC report. The NERC component tof the work if funded through the UKESM multi centre national capability project.
First Year Of Impact 2014
Sector Environment
Description UKESM Mullticentre national capability
Amount £978,127 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2016 
End 03/2021
Title UKESM analysis toolkit 
Description A toolkit of analysis techniques has been shared with collaborating scientists in the Met Office and Reading University. This analysis code forms the basis of the validation tools for the UK Earth System Model (UKESM)'s biogeochemical ocean component (MEDUSA). 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact This toolkit is envisaged to assist with the model development and validation of the UKESM model. The results of the UKESM model runs will be submitted WCRP CMIP6. 
Title Vertically Structure Benthic Model 
Description An explicitly described vertically discretised benthic model has been developed to better resolve chemical gradients and biological response. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact A model based on a more explicit representation of the benthic ecosystem has been developed. Providing an improved ability to explicitly represent processes, compare to observations and resolve sediment chemical gradients this model provides the basis for a number of upcoming studies (as part of MERP, SSB) and is freely available upon request from the author or as a git-repository. 
Title FVCOM Python Toolbox 
Description Python tools for interrogating FVCOM model data. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact Significantly speeds up post-processing model outputs. Also increasing use in parallel processing of outputs and inputs for FVCOM. 
Title FVCOM toolbox 
Description Provide pre- and post-processing tools for the FVCOM hydrodynamic model. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact The toolbox has been included in the official release of FVCOM. 
Description 3rd Carbon from Space Workshop Exeter Jan 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact To explore mechanisms for implementation of the CEOS and GEO recommendations, in collaboration with the Global Carbon Project, the European Space Agency (ESA) is convening the 3rd Carbon form Space workshop bringing together the EO, climate and Earth system science communities addressing the carbon cycle to define a concrete work plan of research and development activities to guide ESA and other space agencies and institutions to respond to the requirements for observations and their exploitation in the time frame 2017-2021.
Year(s) Of Engagement Activity 2015
Description Attended the Offshore Renewable Energy Supergen Hub meeting in London to represent PML's science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Attended the Offshore Renewable Energy Supergen Hub meeting in London to represent PML's science
Year(s) Of Engagement Activity 2017