Interactions between seawater and benthic systems play an important role in global biogeochemical cycling. Benthic fluxes of some chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system (i.e., pH and carbonate saturation state), which in turn modulate the functioning of benthic and pelagic ecosystems. The redox state of the near-bottom layer in many regions can change with time, responding to the supply of organic matter, physical regime, and coastal discharge. We developed a model (BROM) to represent key biogeochemical processes in the water and sediments and to simulate changes occurring in the bottom boundary layer. BROM consists of a transport module (BROM-transport) and several biogeochemical modules that are fully compatible with the Framework for the Aquatic Biogeochemical Models, allowing independent coupling to hydrophysical models in 1-D, 2-D, or 3-D. We demonstrate that BROM is capable of simulating the seasonality in production and mineralization of organic matter as well as the mixing that leads to variations in redox conditions. BROM can be used for analyzing and interpreting data on sediment–water exchange, and for simulating the consequences of forcings such as climate change, external nutrient loading, ocean acidification, carbon storage leakage, and point-source metal pollution.

Sustainable development of the salmon farming industry requires knowledge of the biogeochemical impacts of fish farm emissions. To investigate the spatial and temporal scales of farm impacts on the water column and benthic biogeochemistry, we coupled the C-N-P-Si-O-S-Mn-Fe transformation model BROM with a 2-dimensional benthic-pelagic transport model (2DBP), considering vertical and horizontal transport in the water and upper 5 cm of sediments along a 10 km transect centered on a fish farm. The 2DBP model was forced by hydrophysical model data for the Hardangerfjord in western Norway. Model simulations showed reasonable agreement with field data from the Hardangerfjord in August 2016 (correlations between the model and observations were significant for most variables, and model biases were mostly <35%). The model predicted significant impacts on seafloor biogeochemistry up to 1 km from the fish farm (e.g., increased organic matter in sediments, oxygen depletion in bottom water and sediments, denitrification, metal and sulfur reduction), as well as detectable decreases in oxygen and increases in ammonium, phosphate and organic matter in the surface water near to the fish farm.

Marine biogeochemical processes can strongly interact with processes occurring in adjacent ice and sediments. This is especially likely in areas with shallow water and frequent ice cover, both of which are common in the Arctic. Modeling tools are therefore required to simulate coupled biogeochemical systems in ice, water, and sediment domains. We developed a 1D sympagic–pelagic–benthic transport model (SPBM) which uses input from physical model simulations to describe hydrodynamics and ice growth and modules from the Framework for Aquatic Biogeochemical Models (FABM) to construct a user-defined biogeochemical model. SPBM coupled with a biogeochemical model simulates the processes of vertical diffusion, sinking/burial, and biogeochemical transformations within and between the three domains. The potential utility of SPBM is demonstrated herein with two test runs using modules from the European regional seas ecosystem model (ERSEM) and the bottom-redox model biogeochemistry (BROM-biogeochemistry). The first run simulates multiple phytoplankton functional groups inhabiting the ice and water domains, while the second simulates detailed redox biogeochemistry in the ice, water, and sediments. SPBM is a flexible tool for integrated simulation of ice, water, and sediment biogeochemistry, and as such may help in producing well-parameterized biogeochemical models for regions with strong sympagic–pelagic–benthic interactions.

Interaction between seawater and benthic sediments plays an important role in global biogeochemical cycling. Benthic fluxes of chemical elements (C, N, P, O, Si, Fe, Mn, S) directly affect redox state and acidification (i.e. pH and carbonate saturation), which in turn determine the functioning of the benthic and pelagic ecosystems. The redox state of the near bottom layer can change and oscillate in many regions responding to the supply of organic matter, physical regime and coastal discharge. The goal of this work was to develop a model that captures key biogeochemical processes occurring at the bottom boundary layer and sediment–water interface and analyze the changes that result from seasonal variability in redox conditions in the water column. We used a modular approach allowing the model to be coupled to existing hydrophysical models in 1-D, 2-D or 3-D. The model is capable to simulate seasonality in production and respiration of organic matter as well as in mixing, that leads to variation of redox conditions in the bottom boundary layer. Production and reduction of organic matter and varying redox conditions in the bottom boundary layer affect the carbonate system and lead to changes in pH and alkalinity. Bacteria play a significant role in the fate of organic matter due to chemosynthesis (autotrophs) and consumption of organic matter (heterotrophs). Changes in the bottom boundary layer redox conditions modify the distribution of nutrients (N and P) and redox metals (Mn and Fe). The model can be used for analyzing and interpreting data on sediment-water exchange, and estimating the consequences of forcing such as climate change, external nutrient loading, ocean acidification, carbon storage leakages, and point-source metal pollution.

High alkalinity values on the seaside can influence the exchange of carbon dioxide between seawater and the atmosphere. Still, there are many uncertainties about biogeochemical processes responsible for alkalinity generation in the coastal area. One example of coastal areas with high alkalinity is the German Bight. The German Bight is the south-east part of the North Sea. The literature suggests that high summer alkalinity values in the German Bight result from the exchange of the German Bight with the Wadden Sea (an intertidal zone along Dutch, German, and Danish coasts). We show that the origin of high alkalinity values in the German Bight can be sulfate reduction in sediments of the Wadden Sea and that it can increase alkalinity from March to August up to approximately 220 micromoles per liter. Also, we show that sulfate reduction does not cause any significant year alkalinity flux from the Wadden Sea to the German Bight; instead, nitrogen compounds ( and ) are responsible for it and cause an alkalinity flux about 13 GM a year from the Wadden Sea to the German Bight.

Aquatic biogeochemical processes can strongly interact, especially in polar regions, with processes occurring in adjacent ice and sediment layers, yet there are few modelling tools to simulate these systems in a fully coupled manner. We developed a 1-Dimensional Ice-Pelagic-Benthic transport model (IPBM) for coupled simulation of ice, water column, and upper sediment biogeochemistry. IPBM describes the processes of diffusion and particle sinking in both ice and water, as well sedimentation and bioturbation processes in the sediments. To describe ice, pelagic, and benthic biogeochemical dynamics (reaction terms), IPBM was partly coupled to the European Regional Seas Ecosystem Model (ERSEM) and partly to the Bottom RedOx Model biogeochemistry module (BROM-biogeochemistry) using the Framework for Aquatic Biogeochemical Models (FABM). To test the coupled system, hydrophysical forcing for a site in the Kara Sea area from a Regional Oceanic Modeling System (ROMS) simulation was used. The test run showed reasonable results for all main variables. IPBM reproduces the ice algae bloom in July followed by a pelagic phytoplankton bloom in August–September, as well as seasonal variability of nutrients in the water column.