1. Courtney K. Harris Virginia Institute of Marine Sciences In collaboration with Katja Fennel and Robin Wilson (Dalhousie), Rob Hetland (TAMU), Kevin Xu (CCU). March 3, 2011

2. NO 3 Chlorophyll Large detritus Organic matter N2N2 NH 4 NO 3 Water column Sediment Phytoplankton NH 4 Mineralization Uptake Nitrification Grazing Mortality Zooplankton Susp. particles Aerobic mineralization Denitrification Oxygen Air-sea gas exchange Photosynthetic production Respiration, nitrification Organic matter Sediment Oxygen Consumption Figure from K. Fennel

3. Sediment model ROMS based coupled hydrodynamic – sediment -wave model. Xu, et al. in revision. Model estimates time-averaged for calendar year 1993.

4. Figures from Warner et al. 2008. CSTMS = Community Sediment Transport Modeling System Sediment model uses: Multiple grain sizes. Noncohesive sediment model. Bed layers account for armoring. Sediment Model: CSTMS (ROMS v3.0)

5. Figures from Warner et al. 2008. Sediment routine calculates: Vertical settling; horizontal transport. Accounts for sediment bed layers. Exchange between seabed and water column (erosion and deposition).

6. Based on Soetaert et al. (1996). Overall goal is to improve water column calculations. (adding phosphate and temperature dependence). 1. Add bed_tracers (organic matter, oxygen, nitrate, ammonium, and “ODU”). These interact with water column tracers through diffusion and erosion, and can be buried 2. *Add diffusion between bed layers, and across sediment – water interface. 3. *Add reaction terms to bed_tracers. Model parameters needed for the bed_tracers (like reactivity). Early Diagenesis Model

7. Sea Water Sea Bed Diagenesis: Diffusion and Reactions Sediment-Biology Coupling Dissolved Constituents Bio model has Oxygen, Ammonium, Nitrate, etc. Sediment bed needs Oxygen, Ammonium, Nitrate, “ODU” Turbulent Mixing Tracer Concentrations: Transport and Reactions Diffusion Erosion & Deposition

8. Sediment-Biology Coupling Particulate Classes Organic MatterSediment Sea Water Sea Bed Settling Resuspension De/Sorption Diagenesis Bio model has Large Detritus Small Detritus Sediment model has Particles of varying settling velocities. Sediment bed needs Organic Matter Turbulent Mixing

9. Working within “sedbio_toy” test case. Implemented diffusive mixing within the sediment bed. Added reactive terms to sediment bed tracers (organic matter and oxygen). Current efforts: evaluate simple test cases. Water column Sediment bed. Progress since June, 2010 Variables: oxygen, sediment, organic matter. Exchange through Deposition, Erosion, Diffusion*. CSTMS + Diffusion + Reaction Terms. Reaction, vertical transport: Fennel, and CSTMS.

10. Sediment: Three classes (sand, and Large & small organic matter). Initially have 0.4 g/L in water column. Forcing (365 days): Wind: low – high – low. Temperature: seasonal. Sanity checks: mass conservation. Small Detritus Large Detritus Coarse Sand Test case: SEDBIO_TOY

11. Sediment Bed Profiles (no diffusion or reaction terms) Organic Matter Oxygen Time

12. Diffusion within Sediment Bed Biodiffusive mixing of porewater, and particulate matter. Used implicit, finite volume solution of diffusion equation. Evaluated sensitivity to Depth-dependency of D b. Diffusion coefficient (D b ). Boundary condition at sediment surface. With C. Sherwood (USGS), developed and debugged diffusive mixing code for sediment bed.

13. Sensitivity to D b (porewater oxygen) Increased diffusion coefficient; mixed oxygen further into the bed. Used a depth varying D b. Considered D b from to 8x10 -11 m 2 /s (Morse and Eldridge, 2007). Large D b Small D b

14. Sensitivity to D b (particulate matter) Mass was conserved. Diffusion coefficient could impact erosion depths.

15. Depth dependency in D b Inconclusive whether need to account for depth-dependency of biodiffusion in seabed. Depends on magnitude of biodiffusion, timescale of resuspension and remineralization.

16. Boundary condition at sediment surface Tested sensitivity to diffusion across sediment – water interface. For this test case, both simple end- members produced similar results. Will revisit this question.

17. Developing test cases. This included remineralization of organic matter and biodiffusion (D b = 3 x 10 -12 m 2 /s). Used higher remineralization rate for “large detritus” Testing Reaction Terms for Sediment Tracers

18. Summary and Future Work Began project with ROMS model that included Fennel’s biogeochemistry, and CSTMS sediment. Had non-reactive tracers within the sediment bed. Added biodiffusion within sediment bed. Evaluated diffusion across sediment-water interface. Added decay for porewater oxygen, and organic matter on bed. Ongoing: evaluate sediment bed diffusion and reaction terms. Increase coupling between sediment and biological model. Longer term: add other diagenetic reactions.

19. The End (extra slides follow)

20. From EPA Web-site: http://www.epa.gov/msbasin/hypoxia101.htm Hypoxia 101

21. Coupling of Biogeochemistry and Sediment: Particulate Organic Matter Fennel et al. (2006) specifies particulate organic matter using Large detritus; small detritus (stored in t[i,j,k,itracer]). These interact with other constituents. When they settle to the bed, they are (now) instantly remineralized. Sediment model uses Multiple grain sizes with assigned settling velocities. These can be resuspended (t[i,j,k,ised]); settle to the bed (bed_frac[i,j,kbed,ised], bed_mass[i,j,kbed,ised]), and re-erode. These classes do not interact. To couple these, we defined “bed_tracer[i,j,kbed,isb]” (mmol/m 2 of bed) This stores the deposited particulate organic matter, which can be resuspended. The index isb identifies the constituent (large detritus, small detritus). Particulate “bed_tracer” constituents also must be linked to a sediment class. Each “bed_tracer” will be linked to 1 or more water column tracer(s).