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.
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
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
Organisations
- Plymouth Marine Laboratory (Lead Research Organisation)
- International Nitrogen Management System (Collaboration)
- Scottish Environment Protection Agency (Collaboration)
- MARINE BIOLOGICAL ASSOCIATION (Collaboration)
- University of Liege (Collaboration)
- Joint Nature Conservation Committee (Collaboration)
- Dutch Research Council (Collaboration)
- Helmholtz Association of German Research Centres (Collaboration)
- AGRI-FOOD AND BIOSCIENCES INSTITUTE (Collaboration)
- Natural Resources Wales (Collaboration)
- Meteorological Office UK (Collaboration)
- CENTRE FOR ENVIRONMENT, FISHERIES AND AQUACULTURE SCIENCE (Collaboration)
- Department For Environment, Food And Rural Affairs (DEFRA) (Collaboration)
- NATIONAL OCEANOGRAPHY CENTRE (Collaboration)
- Northern Ireland Department of Agriculture, Environment and Rural Affairs (DAERA) (Collaboration)
- Seafish (Collaboration)
- Xiamen University (Collaboration)
- Environment Agency (Collaboration)
- Italian National Institute of Oceanography and Experimental Geophysics (OGS) (Collaboration)
Publications
Aldridge JN
(2017)
Comparing benthic biogeochemistry at a sandy and a muddy site in the Celtic Sea using a model and observations.
in Biogeochemistry
Atkinson A
(2018)
Comment. What drives plankton seasonality in a stratifying shelf sea? Some competing and complementary theories
in Limnology and Oceanography
Bruggeman J
(2014)
A general framework for aquatic biogeochemical models
in Environmental Modelling & Software
Butenschön M
(2016)
ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels
in Geoscientific Model Development
Ciavatta S
(2016)
Decadal reanalysis of biogeochemical indicators and fluxes in the North West European shelf-sea ecosystem
in Journal of Geophysical Research: Oceans
Holt J
(2017)
Prospects for improving the representation of coastal and shelf seas in global ocean models
in Geoscientific Model Development
Jardine J
(2023)
Rain triggers seasonal stratification in a temperate shelf sea
in Nature Communications
Lessin G
(2019)
Time Scales of Benthic Macrofaunal Response to Pelagic Production Differ Between Major Feeding Groups
in Frontiers in Marine Science
| 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 | citation in FAO-ASIA report |
| Geographic Reach | Asia |
| Policy Influence Type | Citation in other policy documents |
| URL | https://www.fao.org/documents/card/en/c/ca5770en |
| Description | citation in UK POST "Blue carbon" |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| URL | https://post.parliament.uk/research-briefings/post-pn-0651/ |
| 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 | 03/2018 |
| End | 03/2022 |
| Description | Copernicus Marine environment monitoring service (CMEMS) |
| Amount | € 380,000 (EUR) |
| Organisation | Mercator Océan |
| Sector | Private |
| Country | France |
| Start | 04/2015 |
| End | 04/2018 |
| Description | Detection and Attribution of Regional greenhouse gas Emissions in the UK (DARE-UK) |
| Amount | £148,418 (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 | 09/2017 |
| 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 | 09/2017 |
| 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/DMS model developmets |
| Description | The DMSP/DMS 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 22.11 |
| Description | New release of European Regional Seas Ecosystem Model (ERSEM) v22.11 New in this version: Added pelagic denitrification following Sankar et al (2016). Parameterisation of pelagic production and air-sea exchange of nitrous oxide following Lessin et al (2020)(https://doi.org/10.1029/2019JG005613). Added first-order kinetics capability to the pelagic base module. Units of total alkalinity and bioalkalinity have been changed from umol/kg to mmol/m3. Extended documentation with new and updated tutorials. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Not yet |
| URL | https://zenodo.org/record/7300564#.ZA7q3tLP2EI |
| 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 | Microplastic in ERSEM |
| Description | a new module has been developed to simulate transport and sedimetnation of microplastic inside ERSEM |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | the model has been used to provide estimate of efficiency of mussel reef as biofilter for microplastic for Waitrose. |
| 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 | 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 | Dutch Research Council |
| Department | 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 | 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 | 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 | 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 | HBDSEG |
| Organisation | Agri-Food and Biosciences Institute |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Environment Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Joint Nature Conservation Committee |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Marine Biological Association |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | National Oceanography Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Natural Resources Wales |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Northern Ireland Department of Agriculture, Environment and Rural Affairs (DAERA) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Scottish Environment Protection Agency |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | HBDSEG |
| Organisation | Seafish |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I contribute to the evidence group by highlighting the type of evidences that the NERC research community, and in particular the marine modelling community, could provide and by sharing best practices and experience about modelling |
| Collaborator Contribution | they provide a better understanding the requirements of policy makers and management agencies so that my current and future research can have stronger impact |
| Impact | the collaboration is highly multidisciplinary, involving modellers, biologists, ecologists, oceanographers, fishery scientists |
| Start Year | 2020 |
| Description | INMS |
| Organisation | International Nitrogen Management System |
| Sector | Public |
| PI Contribution | I have contributed in writing a section in impact of nitrogen on fisheries on a book that is in preparation. This is part of wider collaboration to work on impact on terrestrial nitrogen pollution on marine ecosystems: we are negotiating a formal involvement in the research |
| Collaborator Contribution | they provided he opportunity to be authors of the section and they will be providing model products on nitrogen discharge from rivers globally to estimate the impact of this in coastal ecosystems |
| Impact | the publication is still being finalised and it is highly multi-disciplinary involving terrestrial, atmospheric, freshwater and marine scientist |
| Start Year | 2019 |
| Description | INMS - INA |
| Organisation | International Nitrogen Management System |
| Sector | Public |
| PI Contribution | I'm collaborating in writing few sections of the International Nitrogen Assessment |
| Collaborator Contribution | I will be contributing to text for the INA and providing model simulations for the marine N budget. |
| Impact | the report are being compiled now, hence no impact has been achieved from the collaboration specifically. however the collaboration is part of the bigger INMS process that has brought the the Colombo declaration on nitrogen management the collaboration is multidisciplinary and involves marine science (physical and biogeochemical oceanography, modelling), freshwater biogeochemistry and modelling, atmospheric chemistry, health science, social science. |
| Start Year | 2020 |
| Description | NPOP - National Partnership for ocean predictions |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I am member of the executive committee and chair of the biogeochemical working group. I contribute in steering UK activities on ocean predictions and how the science community can develop the tools and products to better encounter stakeholders needs. My contribution is mostly focussed on biogeochemical models. |
| Collaborator Contribution | similarly, the other members of the Executive committee contribute with their own expertise on their area of interest with the same common goal |
| Impact | A stakeholder workshop has been held in 2018 and one will be held in 2021 |
| Start Year | 2017 |
| Description | NPOP - National Partnership for ocean predictions |
| Organisation | Meteorological Office UK |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I am member of the executive committee and chair of the biogeochemical working group. I contribute in steering UK activities on ocean predictions and how the science community can develop the tools and products to better encounter stakeholders needs. My contribution is mostly focussed on biogeochemical models. |
| Collaborator Contribution | similarly, the other members of the Executive committee contribute with their own expertise on their area of interest with the same common goal |
| Impact | A stakeholder workshop has been held in 2018 and one will be held in 2021 |
| Start Year | 2017 |
| Description | NPOP - National Partnership for ocean predictions |
| Organisation | National Oceanography Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I am member of the executive committee and chair of the biogeochemical working group. I contribute in steering UK activities on ocean predictions and how the science community can develop the tools and products to better encounter stakeholders needs. My contribution is mostly focussed on biogeochemical models. |
| Collaborator Contribution | similarly, the other members of the Executive committee contribute with their own expertise on their area of interest with the same common goal |
| Impact | A stakeholder workshop has been held in 2018 and one will be held in 2021 |
| Start Year | 2017 |
| 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 | 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 | 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 | 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 | 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 | ERSEM |
| Description | ERSEM: European Regional Seas Ecosystem Model For more information please visit http://ersem.com. Changes since 19.04: Harmonised and extended formulations for air-sea exchange of oxygen and carbon dioxide - with thanks to Phil Wallhead @ NIVA Dissolution of benthic calcite is now dependent on saturation state (this was already the case for pelagic calcite) Fix to prevent spurious oxygen production under heavy deposition at the bed Compatibility with FABM 1.0 |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4075284 |
| Title | ERSEM |
| Description | ERSEM: European Regional Seas Ecosystem Model For more information please visit https://ersem.com. Changes since 20.09: Updated documentation |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4075315 |
| Title | ERSEM |
| Description | ERSEM: European Regional Seas Ecosystem Model For more information please visit https://ersem.com. Changes since 20.09: Updated documentation |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4075283 |
| Title | ERSEM+N-Osmolytes |
| Description | ERSEM: European Regional Seas Ecosystem Model For more information please visit http://ersem.com. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4288840 |
| Title | ERSEM+N-Osmolytes |
| Description | ERSEM: European Regional Seas Ecosystem Model For more information please visit http://ersem.com. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4288841 |
| 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 | Modelling marine benthic ecosystems: from observing state to explaining function - an invited talk at University of Plymouth |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to give a talk at University of Plymouth Earth Science Research Seminar on my work on benthic macrofauna modelling. The talk was well attended by ~100 people - undergraduate and postgraduate students, university stuff - mainly from School of Geography, Earth and Environmental Sciences. The talk was followed by a question session and a follow-up discussion on potential for further collaboration between PML modelling and University of Plymouth Earth Science. |
| Year(s) Of Engagement Activity | 2018 |
| 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 |