ALBERT

Description: Observations indicate that resuspension and associated fluxes of organic material and porewater between the seabed and overlying water can alter biogeochemical dynamics in some environments, but measuring the role of sediment processes on oxygen and nutrient dynamics is challenging. A modeling approach offers a means of quantifying these fluxes for a range of conditions, but models have typically relied on simplifying assumptions regarding seabed–water-column interactions. Thus, to evaluate the role of resuspension on biogeochemical dynamics, we developed a coupled hydrodynamic, sediment transport, and biogeochemical model (HydroBioSed) within the Regional Ocean Modeling System (ROMS). This coupled model accounts for processes including the storage of particulate organic matter (POM) and dissolved nutrients within the seabed; fluxes of this material between the seabed and the water column via erosion, deposition, and diffusion at the sediment–water interface; and biogeochemical reactions within the seabed. A one-dimensional version of HydroBioSed was then implemented for the Rhône subaqueous delta in France. To isolate the role of resuspension on biogeochemical dynamics, this model implementation was run for a 2-month period that included three resuspension events; also, the supply of organic matter, oxygen, and nutrients to the model was held constant in time. Consistent with time series observations from the Rhône Delta, model results showed that erosion increased the diffusive flux of oxygen into the seabed by increasing the vertical gradient of oxygen at the seabed–water interface. This enhanced supply of oxygen to the seabed, as well as resuspension-induced increases in ammonium availability in surficial sediments, allowed seabed oxygen consumption to increase via nitrification. This increase in nitrification compensated for the decrease in seabed oxygen consumption due to aerobic remineralization that occurred as organic matter was entrained into the water column. Additionally, entrainment of POM into the water column during resuspension events, and the associated increase in remineralization there, also increased oxygen consumption in the region of the water column below the pycnocline. During these resuspension events, modeled rates of oxygen consumption increased by factors of up to  ∼  2 and  ∼  8 in the seabed and below the pycnocline, respectively. When averaged over 2 months, the intermittent cycles of erosion and deposition led to a  ∼  16 % increase of oxygen consumption in the seabed, as well as a larger increase of  ∼  140 % below the pycnocline. These results imply that observations collected during quiescent periods, and biogeochemical models that neglect resuspension or use typical parameterizations for resuspension, may underestimate net oxygen consumption at sites like the Rhône Delta. Local resuspension likely has the most pronounced effect on oxygen dynamics at study sites with a high oxygen concentration in bottom waters, only a thin seabed oxic layer, and abundant labile organic matter.

Description: We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean Atmosphere Wave Sediment-Transport Modeling System (COAWST Subversion repository revision 1179). These include: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing non-cohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to the sediment bed-layering scheme that improve the fidelity of the modeled stratigraphic record. Finally, we provide examples of these modules implemented in idealized test cases and a realistic application.

Description: Observations indicate that seabed resuspension of organic material and the associated entrainment of porewater into the overlying water can alter biogeochemical fluxes in some environments, but measuring the role of sediment processes on oxygen and nutrient dynamics is challenging. A modeling approach offers a means of quantifying these fluxes for a range of conditions, but models have typically relied on simplifying assumptions regarding seabed-water column interactions. Thus, to evaluate the role of resuspension on biogeochemical dynamics, we developed a coupled hydrodynamic, sediment transport, and biogeochemical model (HydroBioSed) within the Regional Ocean Modeling System (ROMS). This coupled model accounts for processes including the storage of particulate organic matter (POM) and dissolved nutrients within the seabed; entrainment of this material into the water column via resuspension and diffusion at the sediment-water interface; and biogeochemical reactions within the seabed. A one-dimensional version of HydroBioSed was then implemented for the Rhone Delta, France. To isolate the role of resuspension on biogeochemical dynamics, this model implementation was run for a two-month period that included three resuspension events; also, the supply of organic matter, oxygen and nutrients to the water column was held constant in time. Consistent with time-series observations from the Rhone Delta, model results showed that resuspension increased the diffusive flux of oxygen into the seabed by increasing the vertical gradient of oxygen at the seabed-water interface. This enhanced supply of oxygen to the seabed allowed seabed oxygen consumption to increase, primarily through nitrification. Resuspension of POM into the water column, and the associated increase in remineralization, also increased oxygen consumption in the bottom boundary layer. During these resuspension events, modeled rates of oxygen consumption increased by up to factors of ~ 2 and ~ 8 in the seabed and bottom boundary layer, respectively. When averaged over two months, the intermittent cycles of erosion and deposition led to a 20 % increase of oxygen consumption in the seabed, as well as a larger increase of ~ 200 % in the bottom boundary layer. These results imply that observations collected during quiescent periods, and biogeochemical models that neglect resuspension or use typical parameterizations for resuspension, may underestimate net oxygen consumption at sites like the Rhone Subaqueous Delta. Local resuspension likely has the most pronounced effect on oxygen dynamics at study sites with a high oxygen concentration in the bottom boundary layer, only a thin seabed oxic layer, and abundant labile organic matter.

Description: We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean–Atmosphere–Wave–Sediment Transport Modeling System (COAWST Subversion repository revision 1234). These include the following: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing non-cohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to the sediment bed layering scheme that improve the fidelity of the modeled stratigraphic record. Finally, we provide examples of these modules implemented in idealized test cases and a realistic application.