On the coupling of benthic and pelagic biogeochemical models

Soetaert, Karline; Middelburg, Jack J.; Herman, Peter M. J.; Buis, Kerst

doi:10.1016/s0012-8252(00)00004-0

Cited by 163 publications

(144 citation statements)

References 58 publications

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“…This work clearly demonstrates that water column biogeochemical models on the Peruvian margin require careful consideration of benthic feedbacks to correctly balance nutrient inventories. Biogeochemical models will inaccurately predict feedbacks from the sediment if the seafloor is treated as a simple reflective boundary or ignored altogether; a point made many years ago (Soetaert et al, 2000). It would be instructive to quantify the role of sediments to nutrient budgets on the Peruvian margin using a regional 3-D physicalbiogeochemical model.…”

Section: Discussionmentioning

confidence: 99%

“…Several approaches of varying complexity exist to couple benthic and pelagic models (reviewed by Soetaert et al, 2000). At the one end, time-dependent, vertically-resolved diagenetic models, such as the one presented here, can be coupled to a water column biogeochemistry model (e.g., Archer et al, 2002).…”

Section: Benthic-pelagic Coupling and N Loss On The Marginmentioning

confidence: 99%

“…These allow sediment fluxes to be parameterized using zerodimensional time-dependent approaches (i.e., a single box) at the lower ocean boundary, or by the implementation of transfer functions to predict the immediate response of sediments to changes occurring at the sediment-seawater boundary. These models can be derived from statistical analysis of verticallyresolved benthic models or be purely empirical in nature (Middelburg et al, 1996;Soetaert et al, 2000;Capet et al, 2016).…”

Section: Benthic-pelagic Coupling and N Loss On The Marginmentioning

confidence: 99%

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Strong and Dynamic Benthic-Pelagic Coupling and Feedbacks in a Coastal Upwelling System (Peruvian Shelf)

2017

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Monthly time-series data (1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)) of bottom water oxygen, nitrate and nitrite concentrations from the outer shelf (150 m water depth) in the oxygen minimum zone offshore Peru were coupled to a layered biogeochemical sediment model to investigate benthic-pelagic coupling over multi-annual time scales. The model includes the mineralization of four reactive pools of particulate organic carbon (POC) with lifetimes of 0.13, 1.3, 20, and 1700 year that were constrained using empirical data. Total POC rain rates to the seafloor were derived from satellite based estimates of primary production. Solute fluxes and concentrations in sediment porewater showed highly dynamic behavior over the course of a typical year. Conversion of fixed N to N 2 by denitrification varied from 1.1 mmol m −2 d −1 of N in winter to 1.8 mmol m −2 d −1 of N in summer with a long term mean N loss for the shelf of 1.5 mmol m −2 d −1 of N. Fixed N loss across the whole time-series agreed very well with a previously-published vertically-integrated sediment model for coupling the benthic and pelagic N cycle in regional and global models. Dissimilatory nitrate reduction to ammonium (DNRA) emerges as a major process in the benthic N cycle, producing on average 1.9 mmol m −2 d −1 of ammonium: more than twice the rate of ammonification of organic nitrogen. The model predicts sulfide emissions from the sediment of up to 1 mmol m −2 d −1 when POC rain rate exceeds 20 mmol m −2 d −1 , in agreement with past observations of benthic sulfide fluxes and sulfide plume distributions in the water column. This study demonstrates that sediments on the Peruvian shelf are not static repositories that are independent of changes taking place in the water column. Our results strongly suggest the shelf sediments must exert an important feedback on biogeochemical processes in the overlying waters, and should be considered in regional model studies.

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Section: Discussionmentioning

confidence: 99%

Section: Benthic-pelagic Coupling and N Loss On The Marginmentioning

confidence: 99%

Section: Benthic-pelagic Coupling and N Loss On The Marginmentioning

confidence: 99%

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Strong and Dynamic Benthic-Pelagic Coupling and Feedbacks in a Coastal Upwelling System (Peruvian Shelf)

2017

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“…To ensure conservation of nitrate in the ocean, annual total nitrogen fixation balances denitrification following Lipschultz et al (1990), Middelburg et al (1996), and Soetaert et al (2000). Thus, carbon and nitrogen cycles are partly decoupled.…”

Section: Marine Biogeochemistry Model: Piscesmentioning

confidence: 99%

Skill assessment of three earth system models with common marine biogeochemistry

et al. 2012

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We have assessed the ability of a common ocean biogeochemical model, PISCES, to match relevant modern data fields across a range of ocean circulation fields from three distinct Earth system models: IPSL-CM4-LOOP, IPSL-CM5A-LR and CNRM-CM5.1. The first of these Earth system models has contributed to the IPCC 4th assessment report, while the latter two are contributing to the ongoing IPCC 5th assessment report. These models differ with respect to their atmospheric component, ocean subgrid-scale physics and resolution. The simulated vertical distribution of biogeochemical tracers suffer from biases in ocean circulation and a poor representation of the sinking fluxes of matter. Nevertheless, differences between upper and deep ocean model skills significantly point to changes in the underlying model representations of ocean circulation. IPSL-CM5A-LR and CNRM-CM5.1 poorly represent deep-ocean circulation compared to IPSL-CM4-LOOP degrading the vertical distribution of biogeochemical tracers. However, their representations of surface wind, wind stress, mixed-layer depth and geostrophic circulations (e.g., Antarctic Circumpolar Current) have been improved compared to IPSL-CM4-LOOP. These improvements result in a better representation of large-scale structure of biogeochemical fields in the upper ocean. In particular, a deepening of 20-40 m of the summer mixed-layer depth allows to capture the 0-0.5 lgChl L -1 concentrations class of surface chlorophyll in the Southern Ocean. Further improvements in the representation of the ocean mixedlayer and deep-ocean ventilation are needed for the next generations of models development to better simulate marine biogeochemistry. In order to better constrain ocean dynamics, we suggest that biogeochemical or passive tracer modules should be used routinely for both model development and model intercomparisons.

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“…However, the shelf is a complicated system, and local environmental conditions such as bottom water temperature, oxygen and nutrient concentrations and pelagic primary production inputs are all known to affect biogeochemical cycling within shelf sediments (e.g. Soetaert et al 1996Soetaert et al , 2000Dollar et al 1991;Wijsman et al 1999;Van Cappellen et al 2002;Fulweiler et al 2010;Dale et al 2011). Because the focus of the SSB work is on bed type, these local conditions are considered confounding variables, which can be a particular problem when smaller-scale variables are extrapolated (Morrisey et al 1992).…”

Section: Assessments Of Confounding Variablesmentioning

confidence: 99%

An approach for the identification of exemplar sites for scaling up targeted field observations of benthic biogeochemistry in heterogeneous environments

et al. 2017

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Continental shelf sediments are globally important for biogeochemical activity. Quantification of shelf-scale stocks and fluxes of carbon and nutrients requires the extrapolation of observations made at limited points in space and time. The procedure for selecting exemplar sites to form the basis of this upscaling is discussed in relation to a UK-funded research programme investigating biogeochemistry in shelf seas. A three-step selection process is proposed in which (1) a target area representative of UK shelf sediment heterogeneity is selected, (2) the target area is assessed for spatial heterogeneity in sediment and habitat type, bed and water column structure and hydrodynamic forcing, and (3) study sites are selected within this target area encompassing the range of spatial heterogeneity required to address key scientific questions regarding shelf scale biogeochemistry, and minimise confounding variables. This led to the selection of four sites within the Celtic Sea that are significantly different in terms of their sediment, bed structure, and macrofaunal, meiofaunal and microbial community structures and diversity, but have minimal variations in water depth, tidal and wave magnitudes and directions, temperature and salinity. They form the basis of a research cruise programme of observation, sampling and experimentation encompassing the spring bloom cycle. Typical variation in key biogeochemical, sediment, biological and hydrodynamic parameters over a pre to post bloom period are presented, with a discussion of anthropogenic influences in the region. This methodology ensures the best likelihood of site-specific work being useful for up-scaling activities, increasing our understanding of benthic biogeochemistry at the UK-shelf scale.

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On the coupling of benthic and pelagic biogeochemical models

Cited by 163 publications

References 58 publications

Strong and Dynamic Benthic-Pelagic Coupling and Feedbacks in a Coastal Upwelling System (Peruvian Shelf)

Strong and Dynamic Benthic-Pelagic Coupling and Feedbacks in a Coastal Upwelling System (Peruvian Shelf)

Skill assessment of three earth system models with common marine biogeochemistry

An approach for the identification of exemplar sites for scaling up targeted field observations of benthic biogeochemistry in heterogeneous environments

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