Biogeochemistry, macronutrient and carbon cycling in the benthic layer

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

Abstract

The coasts and shelf seas that surround us have been the focal point of human prosperity and well-being throughout our history and, consequently, have had a disproportionate effect on our culture. The societal importance of the shelf seas extends beyond food production to include biodiversity, carbon cycling and storage, waste disposal, nutrient cycling, recreation and renewable energy. Yet, as increasing proportions of the global population move closer to the coast, our seas have become progressively eroded by human activities, including overfishing, pollution, habitat disturbance and climate change. This is worrying because the condition of the seabed, biodiversity and human society are inextricably linked. Hence, there is an urgent need to understand the relative sensitivities of a range of shelf habitats so that human pressures can be managed more effectively to ensure the long-term sustainability of our seas and provision of societal benefits. Achieving these aims is not straightforward, as the capacity of the seabed to provide the goods and services we rely upon depends on the type of substrate (rock, gravel, sand, mud) and local conditions; some habitats are naturally dynamic and relatively insensitive to disturbance, while others are comparatively stable and vulnerable to change. This makes it very difficult to assess habitat sensitivities or make general statements about what benefits we can expect from our seas in the future.

Recently, NERC and DEFRA have initiated a major new research programme on Shelf Sea Biogeochemistry that will improve knowledge about these issues. In response to this call, we have assembled a consortium of leading scientists that includes microbiologists, ecologists, physical oceanographers, biogeochemists, mathematical modellers and policy advisors. With assistance from organisations like CEFAS, Marine Scotland and AFBI, they will carry out a series of research cruises around the UK that will map the sensitivity and status of seabed habitats based on their physical condition, the microbial and faunal communities that inhabit them, and the size and dynamics of the nitrogen and carbon pools found there. The latest marine technologies will measure the amount of mixing and flow rates just above the seabed, as well as detailed seabed topography. These measurements will allow better understanding of the physical processes responsible for movement and mixing of sediment, nutrient, and carbon. At the same time, cores will be retrieved containing the microbial and faunal communities and their activity and behaviour will be linked to specific biogeochemical responses. Highly specialised autonomous vehicles, called landers, will also measure nutrient concentrations and fluxes at the seabed. Components of the system can then be experimentally manipulated to mimic scenarios of change, such as changing hydrodynamics, disturbance or components of climate change. This will be achieved in the field by generating different flow regimes using a submerged flume or, in the laboratory, using intact sediment communities exposed to different levels of CO2, temperature and oxygen. By measuring the biogeochemical response and behaviour of the microbial and faunal communities to these changes, we will generate an understanding of what may happen if such changes did occur across our shelf seas.

We will use all of this information to assess the relative vulnerability of areas of the UK seabed by overlaying the observation and experimental results over maps of various human pressures, which will be of value to planners and policymakers. Mathematical models will test future scenarios of change, such as opening or closing vulnerable areas to fishing or anticipated changes in the factors that control nutrient and carbon stocks. This will be valuable in exploring different responses to external pressures and for deciding which management measures should be put in place to preserve our shelf seas for future generations.

Planned Impact

The coasts and shelf seas that surround us have been the focal point of human prosperity and well-being throughout our history and, consequently, have had a disproportionate effect on our culture. The societal importance of the shelf seas extends beyond food production to include biodiversity, carbon cycling and storage, waste disposal, nutrient cycling, recreation and renewable energy. Yet, as increasing proportions of the global population move closer to the coast, our seas have become progressively eroded by human activities, including overfishing, pollution, habitat disturbance and climate change. This is worrying because the condition of the seabed, biodiversity and human society are inextricably linked. Hence, there is an urgent need to understand the relative sensitivities of a range of shelf habitats so that human pressures can be managed more effectively to ensure the long-term sustainability of our seas and provision of societal benefits. Achieving these aims is not straightforward, as the capacity of the seabed to provide the goods and services we rely upon depends on the type of substrate (rock, gravel, sand, mud) and local conditions; some habitats are naturally dynamic and relatively insensitive to disturbance, while others are comparatively stable and vulnerable to change. This makes it very difficult to assess habitat sensitivities or make general statements about what benefits we can expect from our seas in the future.

Recently, NERC and DEFRA have initiated a major new research programme on Shelf Sea Biogeochemistry that will improve knowledge about these issues. In response to this call, we have assembled a consortium of leading scientists that includes microbiologists, ecologists, physical oceanographers, biogeochemists, mathematical modellers and policy advisors. With assistance from organisations like CEFAS, Marine Scotland and AFBI, they will carry out a series of research cruises around the UK that will map the sensitivity and status of seabed habitats based on their physical condition, the microbial and faunal communities that inhabit them, and the size and dynamics of the nitrogen and carbon pools found there. The latest marine technologies will measure the amount of mixing and flow rates just above the seabed, as well as detailed seabed topography. These measurements will allow better understanding of the physical processes responsible for movement and mixing of sediment, nutrient, and carbon. At the same time, cores will be retrieved containing the microbial and faunal communities and their activity and behaviour will be linked to specific biogeochemical responses. Highly specialised autonomous vehicles, called landers, will also measure nutrient concentrations and fluxes at the seabed. Components of the system can then be experimentally manipulated to mimic scenarios of change, such as changing hydrodynamics, disturbance or components of climate change. This will be achieved in the field by generating different flow regimes using a submerged flume or, in the laboratory, using intact sediment communities exposed to different levels of CO2, temperature and oxygen. By measuring the biogeochemical response and behaviour of the microbial and faunal communities to these changes, we will generate an understanding of what may happen if such changes did occur across our shelf seas.

Publications

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Payne M (2016) Uncertainties in projecting climate-change impacts in marine ecosystems in ICES Journal of Marine Science: Journal du Conseil

 
Description Strong seasonal patterns occur in the benthic communities within the Celtic Sea. These seasonal differences are strongly influence by sediment type.
Exploitation Route The data are being used by project members to produce papers and refine models. Faunal data will add to our knowledge of the benthic diversity in the Celtic Sea and the health of marine ecosystems.
Sectors Environment

 
Description This project is in it's final year and the data generated by PML are being used in a series of publications are being developed.
First Year Of Impact 2016
Sector Education,Environment
Impact Types Societal

 
Description NERC SSB addition funding
Amount £18,533 (GBP)
Funding ID NE/K002058/1 and NE/K00204X/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2016 
End 09/2016
 
Description The Changing Arctic Ocean
Amount £2,100,000 (GBP)
Funding ID NE/P006434/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 01/2021
 
Title Background values for benthic variables in ERSEM 
Description Added background values to variables of the benthic ERSEM modules. This is one of the original ERSEM features, which is required also in new model structure to allow e.g. recovery of benthic faunal groups. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact Allow modelling of recovery of benthic fauna and bacteria after their elimination due to e.g. stress, trawling, predation. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/tree/V1/SAFE
 
Title Benthic N-cycle DY021 
Description Data on sediment nitrification, denitrification and anammox at four sites in the Celtic Sea (research cruise DY021) Additional work was carried out on advective sediments using flow-through-reactors. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Collaborative work with University of Portsmouth and joint presentation at American Geophysical Union Ocean Sciences 2016 meeting (February 2016, New Orleans, USA) 
 
Title Benthic Survey macrofauna 
Description PML Benthic Survey macrofauna abundance and biomass data from five sites (Cawsand, L4, Rame, Eddystone and E1) and megafauna from one site (L4) in the Western English Channel surveyed between 2008 to 2013 containing data from samples analysed up to and including September 2013 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Contribution to NERC SSB ongoing programme 
URL http://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/03167d6f-a9cd-2e1a-e053-6c86abc0...
 
Title Benthic carbonate system in FABM-ERSEM 
Description Implemented benthic alkalinity fluxes and carbonate system calculations in FABM-ERSEM model framework. Contributions of benthic biogeochemical fluxes to benthic alkalinity are taken into account. Bulk benthic pH and saturation states are calculated, also rough per-layer estimates. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact Benthic carbonate system implementation is a basis for many ocean acidification and CCS impact studies, long-term carbon dynamics modelling in climate scenarios. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/tree/V1/SAFE
 
Title Benthic_N_cycle_DY008 
Description Data on sediment nitrification, denitrification and anammox at four sites in the Celtic Sea (research cruise DY008) 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact This is the first part of a seasonal study of benthic N-cycling in shelf seas. It is expected that this will improve biogeochemical models and thereby our predictive capabilities in shelf seas 
 
Title Composition of active microbial community and micro-eukaryote community in Celtic Sea sediments 
Description Sediments were collected on DY008, DY021, DY030 and DY034 from four contrasting sediment types within the Celtic Sea: mud (station A), sandy mud (station I), muddy sand (station H) and sand (station G). The effect of season and sediment type on the composition of the surficial (top 1 cm) active microbial community was assessed by in depth sequencing of 16S rRNA. For the micro-eukaryote community, 18S rRNA genes were sequenced. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Publications pending 
URL http://www.ncbi.nlm.nih.gov/bioproject/PRJNA401151
 
Title Coupling MEDUSA and ERSEM benthic modules 
Description Incorporation of MEDUSA in FABM framework led to certain degree of modularisation of its code, which allowed to test coupling of its pelagic component with ERSEM benthic modules. The coupled configuration was tested in a global NEMO-FABM-MEDUSA setup (ORCA2). The benefit of coupling is that the lightweight of MEDUSA code suitable for global simulations is combined with considerably more detailed than the default benthic zone description from ERSEM, which will benefit future simulations at a higher resolution and allow better estimates of contribution of shelf seas within the Earth system. Configuration file for MEDUSA-ERSEM is available on PML gitlab server. 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? No  
Impact No impacts so far. 
URL http://gitlab.ecosystem-modelling.pml.ac.uk
 
Title DY_021 SSB Benthic cruise nutrient data 
Description Nutrient data from March 2015 DY_021research cruise on RRS Discovery. Completed, QC'd and submitted to BODC. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Data included in presentation of SSB nutrient data at Ocean Sciences 2016. 
 
Title DY_030 SSB Benthic Cruise nutrient data 
Description Nutrient data from May 2015 DY_030 research cruise on RRS Discovery. Completed, QC'd and submitted to BODC. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Nutrient data presented at the Ocean Sciences meeting in 2016. 
 
Title DY_034 SSB Benthic Cruise nutrient data 
Description Nutrient data from August 2015 DY_034 research cruise on RRS Discovery. Completed, QC'd and submitted to BODC. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Data presented during Ocean Sciences meeting in 2016 
 
Title Diagnostic variables in benthic ERSEM 
Description Added series of individual diagnostic variables (i.e. fluxes) to be added to aggregate diagnostic variables for budget calculations. These include particulate deposition fluxes, suspension-feeding, resuspension fluxes, fluxes of dissolved inorganics and gases, biotic respiration etc. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact Individual diagnostics are necessary for calculation of aggregated diagnostics (fluxes), which will allow estimates of stocks and fluxes of carbon and other elements in North-Atlantic Shelf area, implemented in 3D modelling context. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/
 
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 Epibenthic and infaunal predators in ERSEM 
Description Zoobenthic functional groups of epibenthic and infaunal predators were added to ERSEM. The addition is facilitated through fabm.yaml input and is utilizing generalized structure of model code for benthic fauna. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact More complete representation of benthic faunal functional types in the model. Possibility for implementing the model for benthic biodiversity studies. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/tree/feat/benPred
 
Title Flexible structure for material deposition in ERSEM 
Description Implemented flexible structure for material deposition in ERSEM, allowing arbitrary number of deposition targets defined by model user. Previously this split into benthic organic matter was hardcoded, while new structure is more flexible, allowing partitioning into any number of benthic pools in any proportion. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact New structure allows more flexibility from the user side, better tailoring model structure to research questions. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/
 
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-cycling genes and transcript abundance data in Shelf Sea Biogeochemistry (SSB) 
Description This dataset contains abundances of N-cycling genes and transcripts from microbes collected in the Celtic Sea (April 2014; March 2015; May 2015; August 2015). Sediments were collected from NIOZ cores on Shelf Sea Biogeochemistry (SSB) research cruises DY008, DY021, DY030 and DY034 and transported back to Plymouth Marine Laboratory (PML) where nucleic acid was extracted and quantitative and reverse transcriptase quantitative PCR (qPCR and RTqPCR) measurements of the abundance of key genes and transcripts involved in nitrogen cycling made by Karen Tait. Four contrasting sediment types within the Celtic Sea were compared: mud (station A), sandy mud (station I), muddy sand (station H) and sand (station G). Sediments were sub-sampled from a NIOZ core using 50 mL syringes with the barrel cut off and sectioned into three (0 - 1 cm; 3 - 5 cm and 6 - 8 cm). Five replicate cores were processed for each sediment type. The data were collected as part of the Shelf Sea Biogeochemistry (SSB) research programme as part of the Biogeochemistry, Macronutrient and Carbon Cycling in the benthic layer (BMCC) research programme. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Publications pending 
URL https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/65405342-9048-2068-e053-6c86abc...
 
Title Nutrients for DY008 
Description Nutrient data from the SSB Benthic cruise DY008 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Ongoing data analysis and work-up associated with the ongoing SSB cruises and projects 
 
Title Pelagic to benthic pigment biogeochemistry at the Western Channel Observatory 
Description Pigment data (including alteration products) from the water column and surface sediment at the Western Channel Observatory (site L4) during a prolonged bloom event in 2012. 
Type Of Material Database/Collection of data 
Year Produced 2013 
Provided To Others? Yes  
Impact Presentations at Nereis Park Conference, Challenger Conference for Marine Science and abstract submitted to present this work at ASLO 2015. Publication in review for Progress in Oceanography. 
 
Title Resuspendable fluff layer in ERSEM 
Description A formulation of fluff layer was added to ERSEM model. It represents a layer of freshly sedimented, unconsolidated, easily resuspendable organic matter. It is also available as a food-source to filter-feeding zoobenthos. First-order kinetics of incorporation into consolidated sediment organic matter is implemented. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact Improvement of model performance primarily in shallow coastal regions. Further possibilities for collaborations for improvement of benthic-pelagic coupling in the model. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem/tree/V1/SAFE
 
Title SSB N-cycling genes and transcript abundance during bioturbation (DY021, DY030, DY034) 
Description This data set contains incubations with sediment cores to assess the effect of bioturbating macrofauna on the abundance of genes and transcripts associated with nitrogen cycling. The data were collected between 01-April-2015 to 28-August-2015 over 3 cruises on board the RRS Discovery (DY021, DY030, and DY034) in the Celtic Sea. The authors do not have any concerns over the quality of the data set and values are consistent with similar data reported in the wider literature. Replicate sediment cores (n = 5) of size 20 cm by 20 cm and depth 12 cm were collected from NIOZ cores taken at 4 sites (Muddy, site A; Sandy Mud, site G; Muddy Sand, site H; and Sand, site I). These sediment cores were transferred to clear perspex mesocosms and luminophores, coloured sand which fluoresces under ultra-violet light, were added to guide the selection of undisturbed and bioturbated sediment samples for RNA and DNA molecular analysis. The data were collected as part of the Shelf Sea Biogeochemistry (SSB) research programme as part of Module 3, Task 3.1.1 of the Biogeochemistry, Macronutrient and Carbon Cycling in the benthic layer (BMCC) research programme. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Publications pending 
URL https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/663383d8-6461-7959-e053-6c86abc...
 
Title SSB N-cycling genes and transcript abundance during bioturbation and climate change (DY008) 
Description stract This data set contains data from incubations with sediment cores to assess the impact of ocean acidification (OA) and temperature on the abundance of nitrogen cycling microbes within bioturbated and undisturbed sediments was compared. The data were collected between 01-April-2014 to 10-April-2014 on board the RRS Discovery cruise DY008 in the Celtic Sea. The authors do not have any concerns over the quality of the data set and values are consistent with similar data reported in the wider literature. Intact, undisturbed sediment cores were collected from four contrasting sediment types (mud, sandy mud, muddy sand and sand) and incubated for a period of six months at either 11 deg C/391 ppm pCO2 or 14.5 deg C/1026 ppm pCO2, after which samples were taken from undisturbed surface and from burrowed sediments. The impact of sediment type, sample type and elevated temperature CO2 treatments on the abundance of key genes associated with nitrogen cycling (nitrification, nitrite reductase and anammox) were analysed via quantitative PCR. The data were collected as part of the Shelf Sea Biogeochemistry (SSB) research programme as part of Module 3 of the Biogeochemistry, Macronutrient and Carbon Cycling in the benthic layer (BMCC) research programme. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Publication pending 
URL https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/663383d8-6463-7959-e053-6c86abc...
 
Title SSB benthic N-cycle 
Description This database consists of data collected on the DY008 Shelf Sea Biogeochemistry cruise. Specifically, experimental determination of nitrification, denitrification and anammox rates in sediments. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact This is part of a wider study (Shelf Sea Biogeochemistry) examining the seasonal transformation of Nitrogen in shelf seas. The study is expected to lead to improved understanding, model parameterisation and forecasting capability of biogeochemical cycles which are relevant to climate. 
 
Title Sediment Ammonium Oxidation (Shelf Seas Biogeochemistry) 
Description This dataset describes measurements of Ammonium Oxidation rates in sediments of the Celtic Sea. Data we collected on cruises DY008; DY021; DY030 and DY034. The dataset has been submitted to the British Oceanographic Data Centre (BODC) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This dataset led to a peer-reviewed publication in the journal Biogeosciences discussing Nitrogen cycling in shelf sea sediments. Specifically, this publication estimated the proportions of Nitrogen recycled within and lost from the Celtic Sea. This has implications for marine management, as Nitrogen is the key nutrient sustaining marine productivity. 
 
Title Sediment Denitrification Anammox (Shelf Seas Biogeochemistry) 
Description This dataset describes measurements of Denitrification/Anammox rates in sediments of the Celtic Sea. Data were collected on cruises DY008; DY021; DY030 and DY034. The dataset has been submitted to the British Oceanographic Data Centre (BODC) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This dataset led to a peer-reviewed publication in the journal Biogeosciences discussing Nitrogen cycling in shelf sea sediments. Specifically, this publication estimated the proportions of Nitrogen recycled within and lost from the Celtic Sea. This has implications for marine management, as Nitrogen is the key nutrient sustaining marine productivity. 
 
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 Update of ERSEM formulation on benthic organic matter resuspension 
Description Model formulation of resuspension of benthic semi-labile organic matter was updated to explicitly account for vertical distribution of organic matter in sediments. This improves previous formulation based on concentration of benthic organics and makes use of information available to the model allowing only the uppermost layer of organics to be resuspended at each time instance. 
Type Of Material Computer model/algorithm 
Year Produced 2015 
Provided To Others? Yes  
Impact Improvement of model results on resuspension and consequently on fluxes and transport of particulate and dissolved material. 
URL https://gitlab.ecosystem-modelling.pml.ac.uk/edge/ersem
 
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. 
 
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 CEFAS 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution Bringing together data, novel statistical methods and policy requirements to develop new science. Focusing on benthic systems.
Collaborator Contribution making data available, policy insights, researcher time to develop the work.
Impact Collaboration within research projects; collaboration in ICES WGBIODIV; PhD proposals; collaborative manuscripts; developing policy links for projects
Start Year 2014
 
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 EUROMARINE workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" 
Organisation Ca' Foscari University of Venice
Country Italy 
Sector Academic/University 
PI Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Collaborator Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Impact 1. EGU 2016 session on benthic-pelagic coupling was organised (merged with a session on ocean biogeochemistry due to high amount of contributions to EGU General Assembly). 2. Poster at the EUROMARINE general assembly 2016 3. International multi-disciplinary community on benthic-pelagic coupling was established
Start Year 2015
 
Description EUROMARINE workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" 
Organisation Italian National Institute of Oceanography and Experimental Geophysics (OGS)
Country Italy 
Sector Public 
PI Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Collaborator Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Impact 1. EGU 2016 session on benthic-pelagic coupling was organised (merged with a session on ocean biogeochemistry due to high amount of contributions to EGU General Assembly). 2. Poster at the EUROMARINE general assembly 2016 3. International multi-disciplinary community on benthic-pelagic coupling was established
Start Year 2015
 
Description EUROMARINE workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" 
Organisation Royal Netherlands Institute for Sea Research
Country Netherlands 
Sector Academic/University 
PI Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Collaborator Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Impact 1. EGU 2016 session on benthic-pelagic coupling was organised (merged with a session on ocean biogeochemistry due to high amount of contributions to EGU General Assembly). 2. Poster at the EUROMARINE general assembly 2016 3. International multi-disciplinary community on benthic-pelagic coupling was established
Start Year 2015
 
Description EUROMARINE workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" 
Organisation Utrecht University
Country Netherlands 
Sector Academic/University 
PI Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Collaborator Contribution A foresight workshop "A multi-disciplinary consortium approach for advancement of conceptual frameworks, modelling and experimental approaches to benthic-pelagic coupling" supported by EuroMarine was organized, which initiated collaborative interdisciplinary community.
Impact 1. EGU 2016 session on benthic-pelagic coupling was organised (merged with a session on ocean biogeochemistry due to high amount of contributions to EGU General Assembly). 2. Poster at the EUROMARINE general assembly 2016 3. International multi-disciplinary community on benthic-pelagic coupling was established
Start Year 2015
 
Description Using experimental data for evaluation and improvement of the resuspension component in the ERSEM model 
Organisation University of Portsmouth
Country United Kingdom 
Sector Academic/University 
PI Contribution A joint PML-UoP proposal for supplementary project within NERC/Defra Shelf Sea Biogeochemistry programme was funded.
Collaborator Contribution A joint PML-UoP proposal for supplementary project within NERC/Defra Shelf Sea Biogeochemistry programme was funded.
Impact The main aim of this project is to evaluate and improve the resuspension component of ERSEM model. Evaluation of the model will be done using the observational data obtained from the SSB flume work (and complimented with historical data from other projects). The model will be subsequently parameterized using observed critical shear stresses for the different sediment types.
Start Year 2016
 
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 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