Integrative Modelling for Shelf Seas Biogeochemistry

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

Abstract

Shelf seas are of major societal importance providing a diverse range of goods (e.g. fisheries, renewable energy, transport) and services (e.g. carbon and nutrient cycling and biodiversity). At the same time they are under enormous pressures from man's activities which may have significant impact on the basic function of such systems. For example climate change will lead to large scale changes in stratification and temperature, while increasing atmospheric CO2 levels will lead to acidification of the oceans with significant impacts on ocean biogeochemistry. Simultaneously combinations of direct human activities (e.g. fishing, and eutrophication) directly impact the biogeochemical cycles of carbon and nutrients.

Our understanding of the biogeochemistry of the shelf seas is limited and many processes are poorly understood, in particular the biogeochemical budgets of carbon and nutrients. The key questions include is the UK continental shelf a source or sink for carbon and nitrogen remain unanswered. In addition there are gaps in our knowledge of some of the key physical, chemical and biological controls on biogeochemical cycles. By synthesising empirical knowledge into quantitative descriptions, computer models allow scientists to investigate the functioning of, and interactions between, ecology, biogeochemistry, anthropogenic pressures and climate.

The overarching scientific goal is to enhance our capacity to assess the controls on biogeochemical cycling and hence to quantify with uncertainties the budgets of carbon, nitrogen, phosphorous and silicon including their response to climate, natural variability and anthropogenic stress. The underpinning strategic goal is to develop a new shelf seas biogeochemical model system, coupled to a state of the art physical model, capable of predicting regional impacts of environmental change from days to decades.

We will establish a new common model version for the European Regional Seas Ecosystem Model (ERSEM), drawing from the combined expertise of the partners. Exploiting, existing data, and new biogeochemical process understanding generated by the SSB program we will improve existing process models and develop new ones as appropriate, for both the physical and biological models. We will develop collaborations with the observational and experimentally focussed scientists working on the entire SSB programme in order to make best use of the available expertise. This will form the basis of the new community model system which will be supported and made freely available to the wider UK and international research communities. The resultant model will be used to make simulations of past present and potential future sates of the biogeochemistry of the UK shelf.

In summary, the project will provide new modelling tools which provide estimates of crucial information to help resolve key scientific questions as well as provide a better understanding of the functioning of the shelf seas as they respond to global change and direct anthropogenic pressures. The combination of predictive tools and new knowledge will underpin the development and implementation of marine policy and the implementation of marine forecast systems.

Planned Impact

Impact Summary
Who will benefit from this research?

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

Agencies:
Marine Scotland
AFBI
Marine Climate Change Impacts Partnership (MCCIP)
Marine Management Organisation (MMO)
National Centre for Ocean Forecasting (NCOF)
The international climate evidence community (embodied by the IPCC)

Commercial private sector
Environmental Consultancies

Wider public:
UK and international general public and relevant NGOs

How will they benefit from this research?

Policy-makers/agencies
The Marine Strategy Framework Directive (2008/56/EC) (MSFD) requires EC member states to develop strategies to achieve a healthy marine environment and make ecosystems more resilient to climate change in all European marine waters by 2020 at the latest. The strategies must contain a detailed assessment of the state of the environment, a definition of "Good Environmental Status" (GES) at regional level and the establishment of clear environmental targets and monitoring programmes. Defra, Marine Scotland and AFBI are responsible for the implementation of the MSFD in UK and will benefit from improved knowledge and predictive skill for key indicators of the state of the marine environment. In addition by addressing productivity at the lower trophic levels of the marine food web, including forecasting to century-scales, our research may assist the development of marine fisheries policy and approaches for working towards an ecosystem-focused approach to marine resource management. Cefas are key to this engagement, having for many years advised and Defra (and more recently the MMO) on the environmental status of UK waters and are advising on the implementation of the MSFD and the CFP in England and Wales. DECC and the international climate community (embodied by the IPCC) will benefit through our rigorous investigation and evaluation of shelf seas processes, through engagement with the UK Met Office (UKMO), continuing a close working relationship and the use of a common ocean model, ERSEM-NEMO. This provides the underlying code for operational oceanography (open-ocean and shelf seas) at UKMO, who provide data products to the MOD and to GMES.

Wealth Creation
The European Earth observation program GMES (Global Monitoring for Environment and Security) provides high quality environmental information through the development of a marine monitoring service. Crucially the GMES core service provides regular and systematic reference information on the state of the oceans and regional seas, which is free at the point of use for businesses to exploit commercially. The UKMO run the UK operational ecosystem models delivering high quality data products to the marine core service thought the FP7 MyOCEAN data portal. The model developments proposed will be fed through to the UKMO operational model systems thus improving the range and quality of core service data products.

Wider public
We will publicise our research through:
A project website
Engagement with the media as appropriate
Programme wide outreach activities as they are developed.
Online summaries of the project and key findings disseminated to key interested parties or events

Publications

10 25 50

publication icon
Bruggeman J (2014) A general framework for aquatic biogeochemical models in Environmental Modelling & Software

 
Description European Regional Seas Ecosystem Model (ERSEM) development (Plymouth Marine Laboratory, Cefas) Development of a new modular structure for ERSEM has been ongoing throughout SSB. This allows scientist to remove, add, and duplicate modelled organisms to improve representation of key species and get a clearer picture of the functional biodiversity for a specific ecosystem and/or location. An exciting new development is a size-based module which will represent fish populations. This achievement is a major step forward within the marine ecosystem modelling field, as existing models focus either on the lower or upper trophic levels, and combination of both requires extensive coupling work between two models. Now it will be possible to run ERSEM for the whole of the food web, giving ERSEM a unique ability to explore impacts of climate change and human activity on the whole ecosystem, and resulting impacts on ecosystem functioning (clean water, food supply) and the diversity of marine species.

The representation of the decomposition of organic material in ocean ecosystem models is arguably as important as its creation, since it completes the natural cycle. Timescales are, however, crucially important - affecting spatial patterning of biogeochemical interactions over a range of 3D scales and hence associated feedback processes. For example, the bacterial breakdown of dissolved organic nitrogen (DON) affects the availability of assimilable nitrate, and hence may limit ocean primary production. Joint work between SSB modellers (Work Package 4) and experimentalists investigated the timescales of DON breakdown by the marine bacterium Alteromonas sp: they found5 that this species - although considered to be metabolically versatile - was only able to degrade ~35% of phytoplankton-derived DON over a ~6 month period. In contrast, 75% of dissolved organic carbon (DOC) was used. These effects could be well-simulated by models, and therefore provide opportunities to improve both the generic and site-specific representation of nutrient cycles under current-day condition ? and also in projections of scenario-dependent future conditions.
5 Polimene L, Clark D, Kimmance S & McCormack P (2017) A substantial fraction of phytoplankton-derived DON is resistant to degradation by a metabolically versatile, widely distributed marine bacterium. PLoS ONE 12, e0171391; doi: 10.1371/journal.pone.0171391
The impact of trawling on seabed ecosystems is influenced by the sediment type, geographical location, hydrographic conditions and the gear type used [high]. Implications - MPAs and surrounding areas provide an opportunity to understand the recovery of certain habitat and sediment types in comparison to gear effects. They also provide control areas to enable tracking of seabed baseline changes with climate forcing alone.
Trawling has three main effects on the sediments of shelf seas: (a) changes to the faunal community, (b) resuspension of nutrients into the water column, (c) disturbance induced mixing. [high]. The net effect on carbon storage in shelf sea sediments is largely unknown due to opposing mechanisms of impact. Loss of fauna increases carbon storage whereas resuspension potentially decreases carbon storage. The assessment of trawling impact should move from a focus on faunal structure to a more integrated assessment of benthic biogeochemistry.
The impact of trawling on the faunal community is highly non-linear with trawling effort. An initial trawl pass results in a significant step change in faunal community whereas subsequent passes appear to have less dramatic effects.
Exploitation Route opensurce code with over 200 registered users -
Sectors Environment

URL http://www.pml.ac.uk/Modelling_at_PML/Access_Code
 
Description The current release of ERSEM v15.06 is being transitioned in the operation ocean forecast model of the NW European Shelf by the PML/UKMO as a part of the Copernicus Marine Environment Monitoring Service (CMEMS). The CMEMS service provides operational 3 day forecast of nitrate and chlorophyll for the region. The funding for this service was renewed in March 2018 for another 3 years.
First Year Of Impact 2016
Sector Environment
Impact Types Economic,Policy & public services

 
Description Assessing the combined impact of multiple drivers on the carbon and nutrient budgets of the UK Shelf Seas
Amount £29,507 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2016 
End 02/2018
 
Description CAMPUS (Combining Autonomous observations and Models for Predicting and Understanding Shelf seas)
Amount £501,040 (GBP)
Funding ID NE/R006849/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description Copernicus Marine environment monitoring service (CMEMS)
Amount € 380,000 (EUR)
Organisation Mercator Océan 
Sector Private
Country France
Start 05/2015 
End 04/2018
 
Description Detection and Attribution of Regional greenhouse gas Emissions in the UK (DARE-UK)
Amount £2,500,000 (GBP)
Funding ID NE/S004947/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2019 
End 02/2023
 
Description NERC Industrial CASE Studentship Competition 2017
Amount £90,668 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description SERVICE EVOLUTION OF THE COPERNICUS MARINE ENVIRONNEMENT MONITORING SERVICE
Amount € 116,000 (EUR)
Organisation Mercator Océan 
Sector Private
Country France
Start 03/2015 
End 02/2017
 
Description Shelf Sea Biogeochemistry synthesis workshops
Amount £48,455 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2017 
End 03/2018
 
Description Toward an improved representation of the Fe cycle in ERSEM
Amount £4,200 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 11/2016 
End 11/2016
 
Title PML gitlab server 
Description We set up a gitlab server to help share the model source code and other code between ourselves. We have also added outwards facing components to the server, which allow further collaboration between external scientists. 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact This server has allowed other scientists to access and run the ERSEM model. Over 180 scientists have created accounts on this server, allowing the model and other code to be easily disseminated in the community. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk
 
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. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/ledm/ukesm-validation
 
Title AMM7 hindcast 1981-2015 
Description Hindcast simulation of the marine ecosystem of the NW European Shelf Seas using the last stable releases of NEMO and ERSEM for the years 1981-2015 
Type Of Material Data analysis technique 
Year Produced 2016 
Provided To Others? Yes  
Impact Holistic Information on NW European Shelf Seas for use in NERC's SSB and MERP programs and ReCICLE. 
 
Title AMM7 trawling impact simulation 
Description Simulation of the coupled biogeochemical model NEMO-ERSEM in the Atlantic Margin domain for the period 2000-2015 to assess the impact of trawling 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? Yes  
Impact the model outputs have been used by other scientists in the Marine Ecosystem Research Program. the outputs have also been used presented to Caron Montgomery (head of Marine & Fisheries Evidence team - DEFRA) and used in a scientific workshop on trawling 
 
Title AMM7-V1 hindcast 
Description Simulation of the biogeochemistry of the NorthWestern European Shelf for the period 1981-2015 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact none yet, but the simulation will allow a detailed description of the carbon budget of the UK waters 
 
Title DENITRIFICATION 
Description A formulation describing denitrification has been inserted in the pelagic module of ERSEM. The formulation was derived from the one reported in Vichi et al. (2007). The new model allows the simulation of the bacterial consumption of organic detritus under suboxic and anoxic conditions when bacteria are able to use nitrate (instead of oxygen) for respiration. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact This is a first step toward a more detailed representation on the nitrogen cycle within ERSEM 
 
Title DMS model formulation re-coded in the FABM-ERSEM framework 
Description Model formulation describing DMSP and DMS dynamics (Polimene et al., 2012) have been re-coded in the FABM-ERSEM modelling framework. 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? No  
Impact The DMS(P) model developed at PML (Polimene et al., 2012) is now merged into the latest version of FABM-ERSEM developed in the framework of the Shelf Sea Biogeochemistry (SSB) program . The new FABM-ERSEM has increased modularity allowing a more versatile use of the model. The model code is now usable by the whole ERSEM community, within SSB and beyond. This version of the model will be used as developing platform in the project:' A multidisciplinary study of DMSP production and lysis - from enzymes to organisms to process modelling'. 
 
Title DMSP model developmets 
Description The DMSP model published in 2012 (Polimene at al 2012) was modified extending DMSP production to all the functional types described in the ERSEM model. The model was implemented at L4 station in the Western English Channel and simulation were qualitatively compared with available literature data (Archer et al 2009) 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? No  
Impact This exercise provided a preliminary assessment of model capability to simulate DMSP dynamics in a coastal area 
 
Title Diversified benthic macrofauna structure in ERSEM 
Description ERSEM input files for modelling diversified structure of benthic macrofauna were created. This structure contains 6 functional types compared to classical 2-type implementation in ERSEM. Model results were validated against observational data from Station L4 of the Western Channel Observatory. Functional role of each group within whole ecosystem was analysed. Manuscript describing model setup and results is currently in preparation. 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? No  
Impact This model structure was one of initial steps towards reseach of functional importance of benthic biodiversity using modelling approach, and mutual influence of biodiversity and physical forcing/hydrodynamics. 
 
Title ERSEM 15.06 release 
Description Update of ERSEM model release supported by publication on Geoscientific Model Development Discussions 
Type Of Material Computer model/algorithm 
Year Produced 2014 
Provided To Others? Yes  
Impact The ERSEM model has now a user base of over 100 registered users from all continents of the world and is used as the ecosystem component of CMEMS for the North West European shelf seas. 
URL http://www.shelfseasmodelling.org
 
Title ERSEM 16.06 release 
Description First released of the fully modular FABM compatible ERSEM model 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact Ecosystem model for a wide range of applications from process development over regional to global scale used across the whole worlds (> 200 users). 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/stable/ERSEM/tags/16.06
 
Title ERSEM V1 
Description the new version of ERSEM (ERSEM V1) to be used in the SSB program has been finalised in a new separate branch of the ERSEM repository. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact This version will be used for the delivery of the main outputs of SSB WP4 and SSB WP5 
 
Title Fish in FABM-ERSEM 
Description Ongoing development to add a generic fish compartment in FABM-ERSEM 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact None yet. 
 
Title Improved iron formulation in ERSEM 
Description A new model formulation describing variable iron scavenging rate and bacterial iron uptake has been developed and now is ready to be implemented in the ERSEM code for testing 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Not impacts yet 
 
Title Methane and nitrous oxide cycles in ERSEM 
Description ERSEM model configuration with description of methane and nitrous oxide dynamics. This model version includes cycling of methane utilising hypothesis of production in anoxic micro-niches and production of nitrous oxide as a by-product of nitrification, formulation of air-sea fluxes. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Model results are communicated at various workshops/meetings dedicated to GHG dynamics and impacts. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/commits/ghg_v0
 
Title Model describing the nutrient-dependent production of recalcitrant dissolved organic carbon 
Description By combining previously published model formulations (Polimene et al., 2006 and 2015) we have developed a theoretical modelling framework able to simulate the variability of the Biological Carbon Pump (sinking of particles) to Microbial Carbon Pump (bacterial production of recalcitrant DOM) ratio as function of external nutrient availability 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Outcomes of this model have been published on journal of Plankton Research 
 
Title Model simulations of nitrous oxide and methane dynamics 
Description Decadal simulations (starting at 2000) with NEMO-ERSEM including nitrous oxide and methane cycles over the North-Western Atlantic Shelf (AMM7 domain). 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Simulations performed allow estimates of air-sea fluxes of important greenhouse gases and contribution of the modelled area with respect to global emissions. Spatiotemporal scale of model results allows detailed comparison with existing estimates of saturations, air-sea fluxes and total emissions, which are mainly measurement-based, and temporally and spatially limited. 
 
Title Modelled impact of MPA on recovery of benthic communities from trawling 
Description Several trawling exclusion areas were introduced into NEMO-ERSEM AMM7 model setup with trawling impacts. Model was run for the period 2006-2015. Recovery of benthic fauna within MPAs and in adjacent areas was analysed. 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? No  
Impact The work has potential impact on future policy and management decisions regarding regulations of trawling activity. 
 
Title N fixers module 
Description I expanded the primary producers module of ERSEM in order to simulate nitrogen fixers 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact Extended capability of the UK reference model for Shelf Sea Biogeochemistry 
URL https://gitlab.ecosystem-modelling.pml.ac.uk
 
Title NEMO-FABM-ERSEM coupler 
Description Interface for linking of last stable releases of ERSEM (16.06) and NEMO (3.6). 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact Model infrastructure for operational system of the UK Met Office, NERC's Shelf Seas Biogeochemistry and Marine Ecosystem Program, ReCICLE, CMEMS (NOWMAPS) and various other applications. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/nemo-fabm/NEMO-ERSEM-shelf
 
Title Nitrous oxide in northwest European continental shelf sea - time-varying atmospheric partial pressure 
Description NEMO-ERSEM model with nitrous oxide fluxes included was applied for the AMM7 domain, with time-varying (monthly mean) values of atmospheric partial pressure for nitrous oxide. Model results represent database of N2O concentrations and air-sea fluxes over the period of 2000-2016, with results validated against cruise measurement data. Manuscript discussing model results and analysing factors controlling nitrous oxide air-sea fluxes is currently in preparation. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact This is, to our knowledge, first regional-scale model implementation with process-based formulation of nitrous oxide production and air-sea fluxes. Carefully validated, it a) upscales temporally and spatially sparse measurement data, b) allows analysis of controlling factors and therefore management options, c) creates basis for further development and wider implementation of regional-scale models of nitrous oxide, reducing uncertainty in greenhouse gas emission estimates. 
 
Title PyLag - A tool for modelling particle transport and dispersion in the the marine environment 
Description PyLag is a new particle tracking tool that is written in a mixture of the programming languages Python and Cython. Written using object orientated design principles, it is readily extensible, and can in principle simulate the transport of a range of different particulates, ranging from marine pollutants such as microplastics, to fish larvae. It presently includes support for two different hydrodynamic models: FVCOM and GOTM. However, it is relatively easy to add support for different hydrodynamic models, and it is anticipated support for NEMO will be added in the near future. The model has also been parallelised, and can be used on both desktop computers and modern super computers. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact The model has been used to simulate the transport and dispersal of microplastics around the SW UK coastline, and used to inform field sampling work. Outputs from the model have been used as background material in two Masters projects on microplastics. The model is currently being used by a PhD student at the University of Exeter to simulate the dispersal of Sea Fan larvae. It has also been used to simulate the dispersal of dredged material from various proposed dumping sites near to Plymouth, with results presented to both Cefas and the Marine Management Organisation. 
URL http://www.pml.ac.uk/Modelling/Models/Physical_models_and_couplers
 
Title SSB-ERSEM 14.03 release 
Description Publication of marine biogeochecmical UK community model with full documentation, test harness and test configuration. 
Type Of Material Computer model/algorithm 
Year Produced 2014 
Provided To Others? Yes  
Impact Model suite openly available to registered users with a current user base of >100 form all continents. 
URL http://www.shelfseasmodelling.org
 
Title Simulation of benthic macrofauna dynamics at Station L4 of the Western Channel Observatory 
Description Canonical model of benthic macrofauna based on ERSEM components was created to simulate dynamics of benthic macrofauna at Staion L4 in response to phytoplankton bloom dynamics. The model was used to estimate typical response times of macrofauna, as well as roles of functional types in ecosystem functioning. Manuscript describing this model and its results is currently in revision. 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? No  
Impact The main impact is influence on further integration of different research tools and methods to foster understanding of marine ecosystems. 
 
Title Simulations of benthic macrofaunal diversity in the northwest European shelf seas 
Description NEMO-ERSEM model with diversified benthic macrofauna structure was implemented to simulate dynamics of biodiversity within northwest European continental shelf sea during 2000-2016. Model results allow to analyse how physical forcing and hydrodynamic conditions shape biodiversity structure, which in turn affects biogeochemical cycling within the sea. Model results are currently analysed against available observational data. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact These results allow to analyse how physical environment shapes marine biodiversity, which in turn affects biogeochemistry. This will further allow to analyse impacts of disturbance and climate change on biodiversity and marine ecosystem services in general. 
 
Title Stoichiometric Modulation of Predation (SMP) 
Description The formulation describing the dependency of the zooplankton ingestion and assimilation efficiency on the "food quality" of the prey (Stoichiometric Modulation of Predation SMP, Mitra 2006) has been inserted in ERSEM. Equations 3-5, 8, 9 and 10 of Mitra (2006) have been adapted (accounting for the multi nutrient dynamic explicitly resolved in ERSEM) and incorporated in to the microzooplankton formulation of ERSEM 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Model simulations carried out with the new model (ERSEM+SMP) suggested that after the onset of the proper physical conditions (i.e reduced turbulence and mixed layer depth), phytoplankton decrease in palatability and the subsequent decrease in grazing activity play a significant role in the formation of a bloom. The main output of this work is a conceptual model synergistically combining the abiotic and biotic processes potentially concurring to a phytoplankton bloom formation (Polimene et al., submitted to Progress in Oceanography). 
 
Title Validation of the bacteria module of ERSEM 
Description An ad-hoc experiment has been carried out to validate the bacteria-DOM module of ERSEM. The model demonstrated skills in reproducing DOM degradation dynamics observed in the experiments. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The outcomes of this exercise have been published in Plos One (Polimene et al., 2017). Both experimental data and model simulations have been included in the above mentioned (open access) publication 
URL http://dx.doi.org/10.1371/journal.pone.0171391
 
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 Zooplankton traits 
Description Collection of data regarding traits of zooplankton to later develop a trait based approach for expanding representation of zooplankton in FABM-ERSEM in order to improve diversity and representation of key functions. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Improved communication and linkage with the experimentalist community. 
 
Title trawling effort 
Description Forcing files of bottom trawling effort have been assembled using data provided by CEFAS 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact these files are being used to run scenarios simulation on the impact of bottom trawling on Carbon cycling 
 
Description Biogeochemistry of the benthic zone and implications for marine ecosystems - EGU session 
Organisation University of Liege
Country Belgium 
Sector Academic/University 
PI Contribution A session on biogeochemistry of the benthic zone and implications for marine ecosystems is regularly organised at EGU General Assembly held annually in Vienna. It attracts researchers from various backgrounds - both modellers and experimentalists - to share progress in benthic zone research in oral and poster presentations. Each year prominent speaker is invited to give a keynote talk.
Collaborator Contribution This EGU session will focus on recent outcomes in the understanding of processes controlling benthic biogeochemical cycling and ecosystem dynamics, implementation of new experimental setups and data collection techniques, novel benthic model developments and efforts addressing the implications of benthic-pelagic coupling at a shelf and basin scale. Contributions related to the following non-exhaustive list of sub-topics are particularly encouraged: lability of benthic organic matter, microscale interactions (e.g. microenvironments, burrows, cable bacteria), microphytobenthic primary production, experimental setups and novel data collection techniques (e.g. fixed benthic observatories, eddy-covariance applications), permeability spectrum, extreme and episodic events and ecosystem recovery, erodability and response to resuspension, diversity of benthic habitats.
Impact Ongoing collaboration. No specific outcome yet.
Start Year 2016
 
Description Collaboration with Xiamen University on the theme "microbial carbon sequestration" (International workshop held in November 2018) 
Organisation Xiamen University
Country China 
Sector Academic/University 
PI Contribution MCP project presented to project partner (Xiamen University) in a international wokshop held in China (Xiamen, November 2018)
Collaborator Contribution Xiamen University is one of the world leading institutions in the field of microbial ocean carbon sequestration. They provide useful feedback on how to conduct our experimental work and develop new model formulations.
Impact This collaboration resulted in 4 shared publication (so far).
Start Year 2018
 
Description EGU General Assembly session on benthic processes and benthic-pelagic coupling 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Centre for Ocean Research Kiel
Country Germany 
Sector Public 
PI Contribution Co-organisation and co-chairing a session on benthic processes and benthic-pelagic coupling at the annual EGU General Assembly.
Collaborator Contribution Co-organized a session on benthic processes and benthic-pelagic coupling for the EGU General Assembly 2016.
Impact The session in 2016 was jointly organised and 18 abstracts were received. Due to high amount of total abstracts submitted to EGU and very tight schedule, the session was merged with another session, similar, but more general in scope: OS3.1/BG3.8 Ocean biogeochemistry: novel approaches and synthesis. Poster session on benthic-pelagic coupling had a separate subtitle in the programme. In 2017 the session became a part of a bigger session "Biogeochemistry of coastal seas and continental shelves". This effort is a part of on-going collaborative activities on benthic processes and benthic-pelagic coupling research involving modelling, experimental and observational approaches.
Start Year 2015
 
Description EGU General Assembly session on benthic processes and benthic-pelagic coupling 
Organisation Italian National Institute of Oceanography and Experimental Geophysics (OGS)
Country Italy 
Sector Public 
PI Contribution Co-organisation and co-chairing a session on benthic processes and benthic-pelagic coupling at the annual EGU General Assembly.
Collaborator Contribution Co-organized a session on benthic processes and benthic-pelagic coupling for the EGU General Assembly 2016.
Impact The session in 2016 was jointly organised and 18 abstracts were received. Due to high amount of total abstracts submitted to EGU and very tight schedule, the session was merged with another session, similar, but more general in scope: OS3.1/BG3.8 Ocean biogeochemistry: novel approaches and synthesis. Poster session on benthic-pelagic coupling had a separate subtitle in the programme. In 2017 the session became a part of a bigger session "Biogeochemistry of coastal seas and continental shelves". This effort is a part of on-going collaborative activities on benthic processes and benthic-pelagic coupling research involving modelling, experimental and observational approaches.
Start Year 2015
 
Description EGU General Assembly session on benthic processes and benthic-pelagic coupling 
Organisation Royal Netherlands Institute for Sea Research
Country Netherlands 
Sector Academic/University 
PI Contribution Co-organisation and co-chairing a session on benthic processes and benthic-pelagic coupling at the annual EGU General Assembly.
Collaborator Contribution Co-organized a session on benthic processes and benthic-pelagic coupling for the EGU General Assembly 2016.
Impact The session in 2016 was jointly organised and 18 abstracts were received. Due to high amount of total abstracts submitted to EGU and very tight schedule, the session was merged with another session, similar, but more general in scope: OS3.1/BG3.8 Ocean biogeochemistry: novel approaches and synthesis. Poster session on benthic-pelagic coupling had a separate subtitle in the programme. In 2017 the session became a part of a bigger session "Biogeochemistry of coastal seas and continental shelves". This effort is a part of on-going collaborative activities on benthic processes and benthic-pelagic coupling research involving modelling, experimental and observational approaches.
Start Year 2015
 
Description National Partnership for Ocean Prediction - NPOP 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution I lead the ecosystem models Action Group
Collaborator Contribution the partnership has the aim to promote the use of operational oceanography for marine and maritime policy, management and industries
Impact the partnership organised workshops, conferences and meeting with stakeholders. It is multidisciplnary, involving physical and biological oceanographer, ecosystem modeller, remote sensing scientists and data assimilation scientists
Start Year 2016
 
Description National Partnership for Ocean Prediction - NPOP 
Organisation Meteorological Office UK
Country United Kingdom 
Sector Public 
PI Contribution I lead the ecosystem models Action Group
Collaborator Contribution the partnership has the aim to promote the use of operational oceanography for marine and maritime policy, management and industries
Impact the partnership organised workshops, conferences and meeting with stakeholders. It is multidisciplnary, involving physical and biological oceanographer, ecosystem modeller, remote sensing scientists and data assimilation scientists
Start Year 2016
 
Description National Partnership for Ocean Prediction - NPOP 
Organisation National Oceanography Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution I lead the ecosystem models Action Group
Collaborator Contribution the partnership has the aim to promote the use of operational oceanography for marine and maritime policy, management and industries
Impact the partnership organised workshops, conferences and meeting with stakeholders. It is multidisciplnary, involving physical and biological oceanographer, ecosystem modeller, remote sensing scientists and data assimilation scientists
Start Year 2016
 
Description UK shelf seas modelling consortium 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution Develpoment of the first UK ecosystem community model for shelf seas
Collaborator Contribution Model development, code management and distribution, documentation and licensing.
Impact UK community modelling suite.
Start Year 2013
 
Description UK shelf seas modelling consortium 
Organisation Meteorological Office UK
Country United Kingdom 
Sector Public 
PI Contribution Develpoment of the first UK ecosystem community model for shelf seas
Collaborator Contribution Model development, code management and distribution, documentation and licensing.
Impact UK community modelling suite.
Start Year 2013
 
Description UK shelf seas modelling consortium 
Organisation National Oceanography Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Develpoment of the first UK ecosystem community model for shelf seas
Collaborator Contribution Model development, code management and distribution, documentation and licensing.
Impact UK community modelling suite.
Start Year 2013
 
Description Workshop with experimentalist scientists to develop improved iron formulation 
Organisation National Oceanography Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution The PML modelling group organised a workshop in London (November 2016) to discuss model development with internationally recognised experts in marine Fe-cycle
Collaborator Contribution Experts from NOC (and other institutes) attended the workshop and provided advises on how to improve the current formulation describing iron in ERSEM
Impact Not output/outcomes yet
Start Year 2016
 
Title SSB-ERSEM publication 
Description Publication of UK community model under lesser GPL license 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2014
Licensed No
Impact A userbase of more than 100 users from all fo the globe as been created.
 
Title Generic prokaryote 
Description A new formulation describing the metabolism of a generic, non photosynthetic prokaryote (bacteria and archaea) has been implemented in the European Regional Seas Ecosystem Model (ERSEM). The new formulation implies that different metabolic pathways (aerobic heterotrophy, anaerobic heterotrophy and chemolithotrophy) act simultaneously. However, the relative magnitude of each pathway dynamically varies depending on the environmental conditions (i.e. O2 concentration, DOM and NH4). Thanks to this feature, the model is able to simulate in a dynamic way important processes such as denitrification, nitrification and N2O production. 
Type Of Technology Software 
Year Produced 2015 
Impact The new formulation substantially improves the representation of the nitrogen cycle in ERSEM 
 
Title Shelf Seas Biogeochemistry - ERSEM 
Description The SSB-ERSEM package includes a re-locatable biogeochemical water column model based on GOTM-ERSEM. The code and model setups presented have been developed as a community modelling tool for the NERC Defra UK Shelf Sea Biogeochemistry program. The first release of the model provides a baseline model version upon which we can build and develop new process model descriptions, drawing on the experimental and observational activities undertaken by the wider community. We see developing a better synergy between modelling and experimental studies as key to progress over the next decade, hence this system can by run on a PC and provides an entry level modelling tool for non-specialist modellers to engage in process modelling. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact ERSEM is the ecosystem model component of the UKMO run operational forecast system for the NW European shelf. 
URL http://www.shelfseasmodelling.org/index-en
 
Title Silica dissolution in the water column 
Description A new formulation describing the dissolution of particulate organic silica in the water column has been developed and implemented in the European Regional Seas Ecosystem Model (ERSEM). Silica dissolution is assumed to be dependent on temperature and on the ratio between silica and carbon in the particles. Si:C ratio represents the magnitude of the organic coat which reduces the dissolution of silica (i.e. low Si:C ratios decrease the dissolution rate). In this way, the model accounts for the role played by pelagic bacteria in this process. Bacteria, in fact, are able to increase the Si:C ratio in particulate organic matter by only using C and leaving Si. 
Type Of Technology Software 
Year Produced 2015 
Impact This new development improves the representation of Si dynamics in ERSEM 
 
Title Software Repository 
Description Git-based fully version controlled software code repository with web-interface including wiki and issue tracking system 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact Dissemination of in-house and collaboratively developed software to registered users or general public, enabling collaborative development across centres. 
URL http://gitlab.ecosystem-modelling.pml.ac.uk
 
Description 2nd workshop of the EU Network of Experts for ReDEveloping Models of the European Marine Environment (MEME) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The second workshop of the 'Network of Experts for ReDeveloping Models of the European Marine Environment' was held on 22-23 March 2017 in Brussels, Belgium, jointly organized by DG Environment and DG JRC (Water and Marine Resources Unit) within the framework of the Administrative Arrangement (N110661/ENV.C.2/2016/733192) and the Marine Strategy Framework Directive (MFSD). The aim of this workshop was to continue the information exchange between the Commission and marine modelling experts. Another important objective of this initiative is to narrow the gap between modellers and decision makers in order to better exploit the full utility of models. In this context, the workshop consisted of 17 presentations covering the wide use of marine ecosystem models to address several indicators of the MFSD in coastal zones and European regional seas, including assessment, indicator development and scenario building. The presentations dealt with (1) General lectures, (2) Eutrophication, (3) Hydrography, (4) Higher Trophic Levels and (5) Fish. The participants were invited to join the network informal 'Network of experts on the Modelling of the European Marine Environment (MEME)'. DG Environment and DG JRC emphasized the added value of a joint effort to further develop modelling capabilities with the objective of providing useful advice for policy makers.
Year(s) Of Engagement Activity 2017
 
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
URL http://www.copernicus.eu/events/3rd-carbon-space-workshop
 
Description Dissolved Organic Matter workshop at PML 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact A panel of international researchers from terrestrial, freshwater and marine environments gathered at Plymouth Marine Laboratory for 3 days to discuss current knowledge of Dissolved Organic Matter processing in the environment and identify current gaps. The workshop constituted an excellent event in which all participants tried to find a unifying language to describe the DOM characterisation and transformations from a wide range of disciplines. The output of the workshop was a joined manuscript that aims to unify our current understanding from a generic perspective applicable to multiple disciplines and environments. The manuscript is currently in draft version.
Year(s) Of Engagement Activity 2017
 
Description ICES-WGIPEM presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The presentation, titled "Modelling zooplankton - how and what can we do?" was given at the ICES Working Group on Integrated, Physical-biological and Ecosystem Modelling (WGIPEM). It highlighted the role of zooplankton and the necessity to further develop it's representation in ecosystem models to better characterise ecosystem state and the impact on things like fisheries capacity as it is an important food item for several fishes.
Year(s) Of Engagement Activity 2015
 
Description Invited talk at Earth Science Research seminar at Plymouth University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Presentation "Modelling marine benthic ecosystems: from observing state to explaining function" presenting work on benthic modelling, including L4 benthic fauna modelling with FABM-ERSEM, modelling biodiversity and current issues and future challenges of benthic ecosystem modelling.
Year(s) Of Engagement Activity 2018
URL https://www.plymouth.ac.uk/whats-on/modelling-marine-benthic-ecosystems-from-observing-state-to-expl...
 
Description MSCC/MASTS ecosystem modelling workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact The MSCC Science Alignment Working Group sponsored an initiative to assess UK ecosystem modelling capability and develop a roadmap for the future. This aimed to maximise the uptake of ecosystem models in policy and regulation. This paper is the outcome from a joint MSCC/MASTS workshop on ecosystem modelling that brought together advisors, assessors, biologists, socio-economists, modellers, policy makers, and funders. Here, we describe the future vision and current state, and then outline the roadmap for development of UK ecosystem modelling needed to achieve the future vision.

Workshop help between research community agencies (Cefas, UKMO, Marine Scotland, afbi) defra, mmo etc..
Participated in the steering committee and development of the roadmap. 6 PML staff attended the workshop
Year(s) Of Engagement Activity 2014
 
Description Marine Scotland Science's Scottish Shelf Model workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was an invited speak for Marine Scotland Science's Scottish Shelf Model workshop in Edinburgh, where I presented PML's modelling tools and their use, particularly FVCOM-ERSEM and FVCOM-ERSEM-ShellSIM.
Year(s) Of Engagement Activity 2017
URL http://marine.gov.scot/data/scottish-shelf-model-workshop-june-2017
 
Description NPOP Ocean prediction workshop 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact about 50 people, mostly scientists but also representatives from policy makers and industry. I presented a talk that was well received and sparked discussion. There was also parallel discussion on how improve the uptake of marine biogeochemical models output into policy and management of the marine environment.
Year(s) Of Engagement Activity 2018
 
Description Plymouth Marine Laboratory (PML) welcomes HRH Princess Anne, the Princess Royal 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Plymouth Marine Laboratory (PML) welcomes HRH Princess Anne, the Princess Royal for a guided tour of the laboratory, highlighting its world-class marine research and its plans for the future. Article on PML website and in Devon Life magazine.
Year(s) Of Engagement Activity 2017
URL http://www.pml.ac.uk/News_and_media/News/Plymouth_Marine_Laboratory_(PML)_welcomes_HRH_Prin
 
Description Poster presentation at Challenger Society Conference September 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact "Origin and fate of marine inorganic resources in the North-West European Shelf Seas"
Year(s) Of Engagement Activity 2016
 
Description Presentation at NPOP kick-off 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation of Next Generation Biogeochecmial Modelling System for NW European Shelf
Year(s) Of Engagement Activity 2016
 
Description Presentation of "Shelf Seas: engine of productivity" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact In this meeting the final outcome of the Shelf Sea Biogeochemistry program have been presented to representative of DEFRA and the various DEFRA agencies.
The discussion has been very interesting and alive trying to see how best DEFRA could uptake the new finding from the projects in the policy framework
Year(s) Of Engagement Activity 2018
 
Description Presented PML's work on modelling of carbon in UK waters to Marine Scotland Science. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I gave an overview of PML's work on modelling of carbon in UK waters to Marine Scotland Science.
Year(s) Of Engagement Activity 2017
 
Description Presented PML's work on modelling of carbon in UK waters to the Marine Management Organisation. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact Presented PML's work on modelling of carbon in UK waters to the Marine Management Organisation.
Year(s) Of Engagement Activity 2017
 
Description Royal Society meeting "understanding the European greenhouse gas budget: towards supporting COP21" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact this was the closing meeting of the NERC Greenhouse gas programme. It was a joint science-stakeholder meeting with participants spanning from academics to policymakers to government officers. The discussion was lively and my talk attracted praise from some participants
Year(s) Of Engagement Activity 2017
URL http://www.greenhouse-gases.org.uk/events/understanding-european-ghg-budget-royal-society-8-9-mar-20...
 
Description SSB workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Participants in the workshop got hand on experience with FABM-ERSEM, which provided them with a better understanding of the functioning of ecosystem model and how they can be used. This increased their interest in collaboration with the group for current or future projects.
Year(s) Of Engagement Activity 2015
 
Description Shelf Seas Biogeochemistry Modelling workshops 
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 The workshop will provide participants with an introduction to the ERSEM model, a copy of the code and basic instruction in how to run it. Through participation in conceptual modelling discussion sessions we will foster interactions between the observational and modelling scientists involved in SSB.
Objectives: At the end of the workshop the student will be able to:
1) Knowledge based objectives
a. understand the differences and utility of different type of model (conceptual, numerical , statistical)
b. understand the use and application of numerical models in heuristic and predictive model
c. understand the relevance of ERSEM to their personal science interests.

2) Behavioural objectives
a. make a simple simulation with ERSEM and visualise the results
b. make simple parameter / code changes in ERSEM
Year(s) Of Engagement Activity 2015,2016
 
Description Shelf Seas Biogeochemistry defra briefing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Invited Presentation to Defra on progress with the shelf seas biogeochemistry program, specifically discussing how modelling may help with the implementation and management of marine environmental policy (e.g MFSD).
Year(s) Of Engagement Activity 2015
 
Description Supplied images to a visiting Artist, Cecilia Ramon (Plymouth) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact We were visited by an Artist, Cecilia Ramon, who was interested in using images from our scientific research as inspiration for her work. We provided Cecilia with a set of slides. Cecilia exhibits her work, and through these exhibits we anticipate that our research will reach audiences that may not normally engage with science.
Year(s) Of Engagement Activity 2016
URL http://ceciliaramon.com/
 
Description meeting with Caron Montgomery, head of Marine & Fisheries Evidence team at DEFRA 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact I participated to a meeting with Caron Montgomery to present the highlight of the outcomes of the WP4 of the Shelf Sea Biogeochemistry workshop
Year(s) Of Engagement Activity 2017