1. Development of Coupled Physical and Ecological Models for Stress-Response Simulations of the Apalachicola Bay Regional Ecosystem Co-Principal Investigators: Dr. Mark Harwell Dr. Ping Hsieh Dr. Wenrui Huang Dr. Elijah Johnson Dr. Katherine Milla Dr. Hongqing Wang Dr. Glynnis Bugna Dr. Kevin Dillon Dr. Jack Gentile

2. Research Project Objective: To develop a coupled physical-ecological model of the Apalachicola Bay ecosystem that can be used as a quantitative tool to assess the ecosystem responses to natural and anthropogenic stressors

3. Apalachicola Bay Study Area

9. River Management Forest Management Turbidity Altered Salinity Regime Sedimentation Pathogens Mechanisms: Salinity tolerances Invasive predators Development Navigation Water withdrawals Runoff Erosion Chemical releases Apalachicola Bay Mechanisms: Light availability Mechanisms: Turbidity, Light D.O. Etc. Fire control Harvesting timber Etc. Nutrients Mechanisms: Enrichment Competition Mechanisms: Human consumption issues Oyster Bars Areal extent Productivity, Closures Etc. Inter-Tidal Habitats Areal extent Mosaic, etc. Submerged Aquatic Vegetation Abundance, Distribution Health Water Column Productivity Spp. Composition, Productivity, Etc.. Beach/Dune Habitats Turtles, birds, other species Habitat mosaic Distribution, pattern etc. of habitats Soft-bottom Benthic Communities Infauna Epifauna, etc. Migratory Birds Abundance Distribution Urbanization Septic Runoff Etc.

10. River Water Management Sea-Level Rise Altered Salinity Regime Altered Flow Regime Changes in Water Quality Sedimentation Mechanisms: Burial Suffocation, Gill clogging Mechanisms: Alter sediment type Erosion Altered salinity Development Navigation Water withdrawals Runoff Erosion Chemical releases Apalachicola Bay Salt and Freshwater Marshes Areal Extent Of Marshes Biogeochemical Processes Nutrient dynamics Decomposition, etc. Water Quality Nutrients DO Turbidity, etc. Primary Production Spartina/Typha etc. Productivity Macroinvert. Community Abundance Diversity Selected Species Abundance Health e.g., gators Turtles, Halophytes etc. Mechanisms: Altered mean salinity Altered frequency of low salinity events Mechanisms: Low D.O. Reduced Light Etc. Nursery Function Fish and Invertebrates Exotic Species Abundance Distribution e.g., Phragmites etc.

11. Research Tasks: 1.Adopt 3-D hydrodynamic model to Apalachicola Bay (based on Princeton Ocean Model) 2.Interface hydrodynamic model with EPA WASP WQ Model 3.Calibrate MODBRNCH to Apalachicola River 4.Ecological and WQ data gathering - using existing info, including high-resolution hyperspectral imaging 5.Develop ecological models for salt marsh, oysters, and landscape systems 6.Integrate data and models via GIS data layers 7.Conduct demonstration ecological risk assessment

12. SALT MARSH MODELS OYSTER MODEL HABITAT SUITABILITY MODEL APALACHICOLA BAY LANDSCAPE GIS Modeling Framework for Coupled Apalachicola System RISK ASSESSMENT SCENARIOS APALACHICOLABAY HYDRO- DYNAMIC MODEL APALACHICOLA BAY WATER QUALITY MODEL APALACHICOLARIVER MODEL

13. Characteristics of Apalachicola Bay  Shallow water, multiple tidal boundaries.  Strong freshwater discharge: Q min =155 m 3, Q ave =770 m 3, Q max =2300 m 3.  River discharge perpendicular to the estuarine axis and a long barrier island.  Strong vertical stratification near the river.

14. Multiple tidal forces with different amplitudes

15. Strong Vertical Stratification

16. The Hydrodynamic Model  Princeton Ocean Model (POM) (Blumberg and Mellor, 1987)  Semi-implicit, finite-difference method  Second-order turbulent closure (Mellor and Yamada)

17. Model grid

18. Model Calibration: Surface Elevation at S397

19. Model Calibration: Salinity

20. Tidal Circulation: 12 hr, high

21. Salinity at flood tide

22. SUMMARY Model is calibrated to simulate 3D hydrodynamics and salinity in the Bay. Estuary’s characteristics: a) multiple tidal forces with different amplitudes, b) strong river discharge perpendicular to the estuarine axis, c) shallow water.