1. 1 Columbia River Estuary (CRE) The bioreactor model Tools to implement the bioreactor model in the CRE. An estuarine biogeochemical model for the Columbia River Estuary Clara Llebot, Tuomas Kärnä, Pat Welle, Jesse López, Yvette Spitz, António Baptista

2. 2 The Columbia River Estuary (CRE) One of the major large-river estuaries in the world Salt wedge estuary ~40 km River-dominated estuary. Annual freshet in May-June Ocean end characterized by summer upwelling Low residence time: average 1-5 days Depth (m) 20 15 10 5 2 Baker Bay Cathlamet Bay Youngs Bay North Channel Navigation Channel Grays Bay Columbia River basin

3. 3 The CRE, a bioreactor Estuarine bioreactor: despite the low residence time (1-5 days) significant biogeochemical reactions take place in the estuary. Three hot spots: Lateral bays Estuarine Turbidity Maxima Bloom events (Mesodinium rubrum)

4. 4 Data What allows us to explore the biogeochemistry of the estuary through modeling are the observations: SATURN endurance stations (http://www.stccmop.org/saturn) Field campaigns Gliders, kayak…

5. 5 The SELFE code Mature circulation model. Uses semi-implicit finite-element Eulerian- Lagrangian algorithm to solve the Navier-Stokes equations. Unstructured triangular grids. (Zhang and Baptista 2008)

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7. 7 The bioreactor model Ultimate goal: to understand the main biogeochemical transformations in the estuary (algal blooms, lateral bays, hypoxia, ETM). Must represent –Organic matter –Bacteria –Effects of salinity gradients Based on Spitz 2001 (Bermuda) Adapted to the estuarine environment –Uptake equations adequate for the range of nutrients observed –Mortality and growth rate of phytoplankton salinity dependent –Oxygen Model in progress: benthic remineralization processes, phosphorus, hypoxia Net Ecosystem Metabolism

8. 8 The bioreactor model Oxygen Based on Spitz 2001

9. 9 Phytoplankton growth equations M m, M f = Salinity dependent mortality rate S m, S f = Salinity limitation on growth S opt,m, S opt,f : optimum salinity for growth. dS m, dS f : optimal salinity range. κ m, κ f : salinity at which mortality rate is 0.5. μ 1m, μ 1f : minimum mortality rate. J m, J f : Light limitation*Max. growth rate; Q lim,m, Q fim,f : Nutrient limitation; T m, T f : Temperature limitation; γ 1,m γ 1,f : biomass specific and γ 2,m, γ 2,f, growth specific exudation rates; G 1, G 4, G 6, G 7 : Zooplankton grazing Marine phytoplankton Fresh water phytoplankton

10. 10 Two groups of phytoplankton SPM concentrations have dropped by a factor of 2 or more from pre-dam days to today. Dams stimulate phyto growth in the river. Primary prod. in the Columbia is sensitive to water flow management. Ecological conseq.: freshwater diatom contribution to OM concentrated in the ETM. (Sullivan et al 2001)

11. 11 Configurations of the model Box model SELFE grid (cut at the mouth)Navigational channel grid Challenges from the coupling of biological models to SELFE: High computational times Engage non-modelers: managers and researchers

12. 12 Estuary grid, channel grid, comparison

13. 13 Example of Box Model results Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 5050 4040 3030 2020 1010 0 Nitrate (mmol N/m 3 ) Box model SATURN 03 Surface Bottom

14. 14 SELFE average observed Box model

15. 15 Nitrate in the CRE

16. 16 Applications Sensitivity analysis with box model or channel Net ecosystem metabolism of the estuary Budgets of nitrogen and nutrient transformation Contribution of the lateral bays to the bioreactor Understanding of estuarine species (Mesodinium rubrum) Engagement of Non modelers Joe Needoba Tawnya Peterson Peter Zuber Holly Simmons Byron Crump Brad Tebo Fredrick Prahl Gordon Farquharson Jim Lerczak Craig McNeil Thomas Sanford