Northern Gulf of Mexico: Linking Sediment and Biological Processes within the Regional Ocean Modeling System (ROMS)Courtney K. HarrisVirginia Institute of Marine Sciences

In collaboration with: Kevin Xu (Coastal Carolina University), Katja Fennel (Dalhousie University), Rob Hetland and James Kaihatu (Texas A&M University)

Could not find logos from CCU and Dalhousie.

Mississippi Birdfoot Delta

Atchafalaya Bay

New Orleans

Dead zone: seasonal occurrence of hypoxia

Figure 4 Distribution of frequency of occurrence of mid-summer bottom-water hypoxia over the 60- to 80-station grid from 1985–2001 (updated from Rabalais et al. 1999, Rabalais& Turner 2001b). Star indicates general location of stations C6A and C6B; transect C identified. From Rabalais, Turner, and Wiseman, 2002.

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

Mechanism Contributing to Hypoxia

ROMS Physical, Biogeochemical, and Sediment ModelPhysical model: ROMS v3.0 /3.1Resolution: 3-5 km horizontal, 20 vertical layersForcing: 3-hourly winds; climatological surface heat fluxes; waves from

SWAN run by Kaihatu.River inputs: daily measurements of FW input by U.S. Army Corps of

Engineers; sediment input based on USGS rating curve.

Figure from Hetland and DiMarco, 2007

Model reproduces two dominant modes of circulation (summer and non-summer), weather-band variability and surface salinity fields (Hetland & DiMarco, J. Mar. Syst., 2007)

Biogeochemistry: “FASHAM”, following Fennel et al. 2006.

Sediment: Community Sediment Transport Modeling System (CSTMS), (Warner et al., 2008)

ROMS Physical, Biogeochemical, and Sediment ModelPhysical model: ROMS v3.0 /3.1Resolution: 3-5 km horizontal, 20 vertical layersForcing: 3-hourly winds; climatological surface heat and freshwater

fluxes; waves from SWAN run by Kaihatu.River inputs: daily measurements of FW input by U.S. Army Corps of

Engineers; sediment input based on USGS rating curve.

Figure from Hetland and DiMarco, 2007

Model reproduces two dominant modes of circulation (summer and non-summer), weather-band variability and surface salinity fields (Hetland & DiMarco, J. Mar. Syst., 2007).

Biogeochemistry: “FASHAM”, following Fennel et al. 2006.

Sediment: Community Sediment Transport Modeling System (CSTMS), (Warner et al., 2008).

NO3

Chlorophyll

Largedetritus

Organic matter

N2 NH4 NO3

Water column

SedimentSediment

Phytoplankton

NH4

Mineralization

Uptake

Nitrification

Nitrification

Grazing

Mortality

Zooplankton

Susp.particles

Aerobic mineralizationAerobic mineralizationDenitrificationDenitrification

Biological model: nitrogen cycling in water column and simplified sedimentary processes; oxygen coupled (Fennel et al., GBC, 2006)River inputs: USGS nutrients fluxes for Mississippi and Atchafalaya

Current limitations: no explicit sediment (instantaneous remineralization), no sediment transport, no P-cycle

Coupled Physical – Biological Model

Model ran to represent 1990 – 1999.

Provided realistic estimates of hypoxic area.

Next step: improve treatment of biogeochemical constituents on the sediment bed.

Figure: Frequency of occurrence of hypoxia in the realistic coupled physical/biological simulation with NO3 and PON inputs for June (top), July (middle), and August (middle). Model statistics based on 10-year simulation.

From Katja Fennel, Dalhousie University.

June

July

August

Coupled Physical – Biological Model

Model ran to represent 1990 – 1999.

Provided realistic estimates of hypoxic area.

Next step: improve treatment of biogeochemical constituents on the sediment bed.

Figure: Frequency of occurrence of hypoxia in the realistic coupled physical/biological simulation with NO3 and PON inputs for June (top), July (middle), and August (middle). Model statistics based on 10-year simulation.

From Katja Fennel, Dalhousie University.

June

July

August

Rabalais, Turner, and Wiseman, 2002.

ROMS Physical, Biogeochemical, and Sediment ModelPhysical model: ROMS v3.0 /3.1Resolution: 3-5 km horizontal, 20 vertical layersForcing: 3-hourly winds; climatological surface heat and freshwater

fluxes; waves from SWAN run by Kaihatu.River inputs: daily measurements of FW input by U.S. Army Corps of

Engineers; sediment input based on USGS rating curve.

Figure from Hetland and DiMarco, 2007

Model reproduces two dominant modes of circulation (summer and non-summer), weather-band variability and surface salinity fields (Hetland & DiMarco, J. Mar. Syst., 2007).

Biogeochemistry: “FASHAM”, following Fennel et al. 2007.

Sediment: Community Sediment Transport Modeling System (CSTMS), (Warner et al., 2008).

Sediment Model: CSTMS (ROMS v3.0)

Figures from Warner et al. 2008.

• Noncohesive sediment model.• Multiple grain sizes.• Bed layers account for armoring.• Two sediment sources:

- Rivers (Atchafalaya and Mississippi).- Seabed erosion.

Sediment routine calculates:• Vertical settling.• Keeps account of sediment bed

layers.• Exchange between seabed and

water column (erosion and deposition).

0

20

40

60

80

100

-94 -93 -92 -91 -90 -89 -88

27.5

28

28.5

29

29.5

30

30.5Sediment type, mud%

longitude

latit

ude

Sediment PropertiesSediment Type τcr (Pa) Ws (mm/s) Fraction

Mississippi Large Flocs 0.08 1 80%

Small Flocs 0.03 0.1 20%

Atchafalaya Large Flocs 0.08 1 80%

Small Flocs 0.03 0.1 20%

Sea bed Sand 0.12 10 SpatiallyVariableMud 0.10 1

20m

50m100m

300mSandy

Muddy

US Seabed Data from Jeff Williams (USGS) and Chris Jenkins (INSTAAR)

Trinity ShoalShip Shoal

This sediment model

presented at Ocean Sciences, March 2008, by

Kevin Xu.

0

10

20

30

01234

0

1

2

3x 10

9 Water Discharge (m3/day)

MississippiAtchafalaya

01/01 04/01 07/01 10/010

5

10

15x 10

5

Day of year 1993

Sediment Discharge (tons/day)

MississippiAtchafalaya

Wind, Wave, Water and Sediment Discharge in 1993

(USGS discharge data from C. Demas and B. Meade)

‘Storm of Century’ LATEX tetrapod observation

Wind Speed (m/s) and SWAN Wave Height at Tetrapod (m)

Model estimates for 1993 storm.

This sediment model

presented at Ocean Sciences, March 2008, by

Kevin Xu.

Estimates for 1993On average, currents flow

westward along coast.

Wave resuspension significantly impacts sediment resuspension.

Fluvial material from the Atchafalaya and Mississippi mix on the Louisiana shelf.

28

29

30

latit

ude

Deposition of Mississippi Sediment, log10

kg/m2

-6

-4

-2

0

2

28

29

30

latit

ude

Deposition of Atchafalaya Sediment, log10

kg/m2

-6

-4

-2

0

2

-94 -93 -92 -91 -90 -89 -8828

29

30

Longitude

latit

ude

Deposition of Mississippi and Atchafalaya, log10

kg/m2

-6

-4

-2

0

2

Storm of the Century (March 12 – 16, 1993)

Salinity

Mean Current

Near-bedSuspendedSediment

Wave Height

(1)

10 12 14 16 18 20-10

-5

0

5

10

15

20

25

Mar1993

Win

d S

pe

ed

, m/s

(1)

(2)

(3)

Current-wave dominated

Low-medium water dischargeStrong winds

Three Phases

Salinity,Mean Current,Wind

Wave Height

Storm of the Century

Onshore Transport Along-Shore Transport

(3)(2)

Near-bedCurrent

SuspendedSediment

Storm of the Century

Deposition

Erosion

Erosion/Deposition relative to river sediment on the sea bed on Mar/12/1993

On shore sediment transport during cold fronts (Kineke et al., 2006, CSR) Facilitate on-shore accumulationMay set the stage for summertime hypoxia.

(log10 kg/m2)

Peak of Storm

Post Storm

LATEX (May-June, 1993)River-dominated

High water dischargeWeak winds

LATEX tetrapod(see Wright, et al. 1997)

Stratified water columnHorizontal sediment advection

B

B’

B B’

30 psu isohaline

Comparison of Model to LATEX Data

1. Near bottom flows

This Model

(Wright et al, 1997, MG)

16 19 22 25 28 31 3 6 9 12 15-0.04

-0.02

0

0.02

0.04

0.06

May Jun1993

Nea

r bo

ttom

flo

w,

m/s 100 cm above sea bed

2. Wave Orbital Speed

3. Sediment Concentration

Sediment Model: Conclusions• Waves increased sediment concentration and dispersal, and

facilitated on-shore accumulation offshore of Atchafalaya Bay.

• During the ‘Storm of the Century’, currents and waves dominated transport. Water column was well mixed and sediment was eroded from middle shelf and deposited on the inner shelf. Net shoreward flux of sediment.

• During ‘Calm LATEX’ conditions, river plumes dominated transport in stratified water. Currents and waves occasionally resuspended sediment. Model showed reasonable agreement to tetrapod data.

• Both Mississippi and Atchafalaya sediment contributed to turbidity south of the Atchafalaya Bay.

Sediment-Biology CouplingOngoing work

(Fennel et al., 2006, GBC)

At least 13 tracers

TemperatureSalinity

Large floc sed.Small floc sed.Sand

NitrateAmmoniumChlorophyllPhytoplanktonZooplanktonLarge DetritusSmall DetritusOxygen

(Warner et al., 2008)

Organic Matter Flocs

Sea Water

Sea Bed

Settling

Resuspension

Partition & Aggregation

Diagenesis

Sediment-Biology Coupling

Bio model hasLarge DetritusSmall Detritus Sediment model has

Large FlocsSmall Flocs

Sediment bed needsOrganic Matter

Organic Matter Flocs

Sea Water

Sea Bed

Settling

Resuspension

Partition & Aggregation

Diagenesis

Sediment-Biology Coupling

Bio model hasOxygen, Ammonium, Nitrate

Sediment bed needsOxygen, Ammonium, Nitrate, “ODU”

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▫ Large flocs; small flocs.▫ 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/km2 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).

SEDBIO TOYOne dimensional model that has

particulate organic matter.

Large detritus linked to large floc.

Small detritus linked to small floc.

When detritus settles: it adds to bed_tracer(i,j,kbed=1,itracer=“organic matter”).

When organic matter erodes: it adds to t(i,j,k=1,itracer=detritus).

At present, neglect any interactions between detrital classes on the bed.

SEDBIO Toy Test: Conservation• One-dimensional

sediment & water column.

• Suspended detritus settles and adds to bed mass.

• Winds increase; detritus resuspended.

• Winds decrease and material redeposits.

• Organic matter is conserved.

Early Diagenesis ModelNext: Following model developed

by Soetart et al. (1996).

1.Add other bed_tracers (oxygen, nitrate, ammonium, and “ODU”).• These will interact with water

column tracers through diffusion, burial, and erosion.

2.Add reaction terms to bed_tracers.• Model parameters needed for the

bed_tracers (like reactivity). • Bed diffusivity will need to be

added.

3.The goal here is to improve the water column calculations.

Challenges and Issues• Run-time: computational limits are always present, this

will need to track at least 15 tracers.

• Need to work within cohesive bed model.

• Will likely stress some parts of the sediment model that have not been tested or developed (Porosity? Biodiffusion?)

• Inherent mis-match in spatial scales / temporal scales between sediment dynamics and diagenesis(?).

• Will we have data to set model parameters, and for validation?

Summary

• The MCH (Mechanisms Controlling Hypoxia) modeling group has produced coupled physical – sediment; and physical – biological models; both of which seem to be working well.

• At present, particulate organic matter in the sediment routine has been linked to water column detritus.

• Efforts to link other water column tracers to the seabed will face some challenges but the goal is to improve on the current simplistic assumptions used in the biology model.

THE END