courtney k. harris virginia institute of marine sciences in collaboration with katja fennel and...
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![Page 1: Courtney K. Harris Virginia Institute of Marine Sciences In collaboration with Katja Fennel and Robin Wilson (Dalhousie), Rob Hetland (TAMU), Kevin Xu](https://reader035.vdocuments.net/reader035/viewer/2022062518/56649ea85503460f94bac8ec/html5/thumbnails/1.jpg)
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
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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
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(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.
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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)
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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).
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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
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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
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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
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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.
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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
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Sediment Bed Profiles (no diffusion or reaction terms)Organic Matter Oxygen
Time Time
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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
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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
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Sensitivity to Db(particulate matter)Mass was conserved.Diffusion coefficient could
impact erosion depths.
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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.
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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.
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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
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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.
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From EPA Web-site: http://www.epa.gov/msbasin/hypoxia101.htm
Hypoxia 101
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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).