courtney k. harris virginia institute of marine sciences in collaboration with katja fennel and...
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Courtney K. HarrisVirginia Institute of Marine Sciences
In collaboration with Katja Fennel and Robin Wilson (Dalhousie), Rob Hetland (TAMU), Kevin Xu (CCU).
March 3, 2011
NO3
Chlorophyll
Largedetritus
Organic matter
N2 NH4 NO3
Water column
Sediment
Phytoplankton
NH4
Mineralization
Uptake
Nitrification
Nitrification
Grazing
Mortality
Zooplankton
Susp.particles
Aerobic mineralizationDenitrification
Oxygen
Air-sea gas exchange
Photosynthetic production
Respiration,nitrification
Organic matter
Sediment Oxygen Consumption
Figure from K. Fennel
(A) Surface Salinity & Mean Current
(ppt)
Current, 0.2 m/s28
N
29N
30N
0
10
20
30
(B) Near-bed Wave Velocity
(m/s)
28N
29N
30N
0.05
0.1
(C) Wave Height
(m)
28N
29N
30N
0
0.5
1
94W 93
W 92
W 91
W 90
W 89
W 88
W
28N
29N
30N (D) Suspended Sediment
(log10
kg/m2)
-6
-4
-2
0
Sediment modelROMS based coupled
hydrodynamic – sediment -wave model.
Xu, et al. in revision.
Model estimates time-averaged for calendar year 1993.
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)
Sediment Model: CSTMS (ROMS v3.0)
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).
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
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
Sediment-Biology CouplingParticulate Classes
Organic Matter Sediment
Sea Water
Sea Bed
Settling
Resuspension
De/Sorption
Diagenesis
Bio model hasLarge DetritusSmall Detritus Sediment model has
Particles of varying settling velocities.
Sediment bed needsOrganic Matter
Turbulent Mixing
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 colum
nS
ediment bed.
Progress since June, 2010Variables: oxygen, sediment, organic matter.
Exchange through Deposition, Erosion, Diffusion*.
CSTMS + Diffusion + Reaction Terms.
Reaction, vertical transport: Fennel, and CSTMS.
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 DetritusLarge DetritusCoarse Sand
Test case: SEDBIO_TOY
Sediment Bed Profiles (no diffusion or reaction terms)Organic Matter Oxygen
Time Time
Diffusion within Sediment BedBiodiffusive mixing of
porewater, and particulate matter.
Used implicit, finite volume solution of diffusion equation.
Evaluated sensitivity to Depth-dependency of Db.
Diffusion coefficient (Db).Boundary condition at
sediment surface.
With C. Sherwood (USGS), developed and debugged diffusive mixing code for sediment bed.
;itrc itrcb
bed bed
c cD
t z z
Sensitivity to Db(porewater oxygen)
Increased diffusion coefficient; mixed oxygen further into the bed.
Used a depth varying Db.Considered Db from to
8x10-11 m2/s (Morse and Eldridge, 2007).
Large Db
Small Db
Sensitivity to Db(particulate matter)Mass was conserved.Diffusion coefficient could
impact erosion depths.
Depth dependency in DbInconclusive whether
need to account for depth-dependency of biodiffusion in seabed.
Depends on magnitude of biodiffusion, timescale of resuspension and remineralization.
Boundary condition at sediment surfaceTested sensitivity to
diffusion across sediment – water interface.
For this test case, both simple end-members produced similar results.
Will revisit this question.
Developing test cases.This included remineralization of
organic matter and biodiffusion (Db = 3 x 10-12 m2/s).
Used higher remineralization rate for “large detritus”
Testing Reaction Terms for Sediment Tracers
Summary and Future WorkBegan 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.
From EPA Web-site: http://www.epa.gov/msbasin/hypoxia101.htm
Hypoxia 101
Coupling of Biogeochemistry and Sediment: Particulate Organic MatterFennel 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 usesMultiple 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/m2 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).