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).