scholarly journals Bottom RedOx Model (BROM, v.1.0): a coupled benthic-pelagic model for simulation of seasonal anoxia and its impact

2016 ◽  
Author(s):  
E. V. Yakushev ◽  
E. A. Protsenko ◽  
J. Bruggeman ◽  
R. G. J. Bellerby ◽  
S. V. Pakhomova ◽  
...  
Keyword(s):  
Boundary Layer ◽  
Organic Matter ◽  
Redox State ◽  
Nutrient Loading ◽  
Chemical Elements ◽  
Bottom Layer ◽  
Redox Conditions ◽  
Bottom Boundary Layer ◽  
Bottom Boundary ◽  
Benthic Sediments

Abstract. 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.

scholarly journals Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry

2017 ◽  
Vol 10 (1) ◽  
pp. 453-482 ◽  
Author(s):  
Evgeniy V. Yakushev ◽  
Elizaveta A. Protsenko ◽  
Jorn Bruggeman ◽  
Philip Wallhead ◽  
Svetlana V. Pakhomova ◽  
...  
Keyword(s):  
Organic Matter ◽  
Redox State ◽  
Nutrient Loading ◽  
Chemical Elements ◽  
Bottom Layer ◽  
Saturation State ◽  
Biogeochemical Models ◽  
Sediment Biogeochemistry ◽  
Marine Carbonate ◽  
Mineralization Of Organic Matter

Abstract. 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.

scholarly journals The Roles of Resuspension, Diffusion and Biogeochemical Processes on Oxygen Dynamics Offshore of the Rhone River, France: A Numerical Modeling Study

2016 ◽  
Author(s):  
Julia M. Moriarty ◽  
Courtney K. Harris ◽  
Christophe Rabouille ◽  
Katja Fennel ◽  
Marjorie A. M. Friedrichs ◽  
...  
Keyword(s):  
Boundary Layer ◽  
Organic Matter ◽  
Oxygen Consumption ◽  
Water Column ◽  
Bottom Boundary Layer ◽  
Water Interface ◽  
Bottom Boundary ◽  
Rhône Delta ◽  
Oxygen Dynamics

Abstract. 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.

scholarly journals Man-Induced Discrete Freshwater Discharge and Changes in Flow Structure and Bottom Turbulence in Altered Yeongsan Estuary, Korea

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1919 ◽  
Author(s):  
KiRyong Kang ◽  
Guan-hong Lee
Keyword(s):  
Boundary Layer ◽  
Surface Layer ◽  
Flow Structure ◽  
Bottom Layer ◽  
Sediment Concentration ◽  
Freshwater Discharge ◽  
Bottom Boundary Layer ◽  
Maximum Magnitude ◽  
Flow Measurements ◽  
Bottom Boundary

Flow measurements were performed in the altered Yeongsan estuary, Korea, in August 2011, to investigate changes in flow structure in the water column and turbulence characteristics very close to the bed. Comparison between the bottom turbulent kinetic energy (TKE) and suspended sediment concentration (SSC) was conducted to examine how discrete freshwater discharge affects the bottom sediment concentration. The discrete freshwater discharge due to the gate opening of the Yeongsan estuarine dam induced a strong two-layer circulation: an offshore-flowing surface layer and a landward-flowing bottom layer. The fine flow structure from the bed to 0.35 m above the bottom (mab hereafter) exhibited an upside-down-bell-shaped profile for which current speed was nearly uniform above 0.1 mab, with the magnitude of the horizontal and vertical flow speeds reaching 0.1 and 0.01 m/s, respectively. The bottom turbulence responded to the freshwater discharge at the surface layer and the maximum magnitude of the Reynolds stress reached up to 2 × 10−4 m2/s2 during the discharged period, which coincided with increased SSC in the bottom boundary layer. These results indicate that the surface freshwater discharge due to opening of the estuarine dam gate increases the SSC by the discharge-induced intensification of the turbulent flow in the bottom boundary layer.

Overturning and Dissipation Caused by Baroclinic Tidal Flow near the Sill of a Fjord Basin

2009 ◽  
Vol 39 (9) ◽  
pp. 2156-2174 ◽  
Author(s):  
Lars Arneborg ◽  
Bengt Liljebladh
Keyword(s):  
Boundary Layer ◽  
Time Series ◽  
Large Fraction ◽  
Internal Tide ◽  
Bottom Layer ◽  
Internal Tides ◽  
Bottom Boundary Layer ◽  
Transitional Flow ◽  
Mixing Efficiency ◽  
Bottom Boundary

Abstract Dissipation time series and moored velocity and density time series on the inner slopes of the Gullmar Fjord sill showed that the internal tides generated at the sill radiated to the head of the fjord, were reflected, and then radiated back to the sill, where they dissipated their energy mainly below sill level. A large amount of the dissipation was caused by a transitional flow at a particular phase of the internal tide, when the bottom layer descended down the sill slope and had to pass a constriction set up by a submarine hill. The inward, baroclinic bottom-layer flow transformed into a supercritical bottom jet, which separated from the bottom just downstream of the constriction. A large fraction of the dissipation took place in the successive rebounding region (the hydraulic jump) above the bottom jet, where overturns of the same size as the vertical extent of the rebounding region were observed. More than half of the dissipation was happening in the bottom boundary layer below the jet. During the transitional flow, there were clear pulsations of the jet with periods of about 15 min. The amount of diapycnal mixing caused by the turbulence was reduced by the large fraction of dissipation within the bottom boundary layer and perhaps also by the high-buoyancy Reynolds numbers within the rebounding region. When using a relatively new parameterization of mixing, the mixing was significantly reduced compared to using the traditional constant mixing efficiency method.

Sign in / Sign up

Export Citation Format

Share Document