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