Tidal Flat Estuaries

I: Description of the Ecosystem.- 1 Modelling the Ecosystem of the Ems Estuary.- 1.1 Introduction.- 1.2 Earlier Investigations of the Ems Estuary.- 1.3 Other Models of the Ems Estuary.- 1.4 Structure of the Ecosystem Model.- 1.5 A Glimpse of the Modelling Practice.- 1.6 Simulation Hard-and Software.- 2 The Abiotic Environment.- 2.1 History.- 2.2 Topography and Morphology.- 2.3 Sediment Composition.- 2.4 Climate.- 2.5 Fresh Water Supply.- 2.6 Tide.- 2.7 Water Movement and Mixing.- 2.8 Sediment Transport and Accumulation.- 2.9 Nutrients.- 3 Biology.- 3.1 General Description of the Estuary.- 3.2 The Pelagic System.- 3.3 The Benthic System.- 3.4 The Epibenthic System.- 4 General Features in the Model.- 4.1 Universal Biological Processes.- 4.1.1 Maintenance Processes.- 4.1.2 Activity-Dependent Processes.- 4.1.3 Bookkeeping Calculations.- 4.1.4 Modelling Food Uptake.- 4.1.5 Food Selection.- 4.1.6 Food Levels.- 4.2 Compartments and Boundary Conditions.- 4.2.1 Boundaries.- 4.2.2 The Dimensions of the Compartments.- 4.2.3 Boundary Conditions.- 4.3 Forcing Functions.- 4.3.1 Temperature.- 4.3.2 Irradiance.- 4.4 The Nature and Flux of Organic Matter.- 4.4.1 Partition of Organic Matter.- 4.4.2 Transport of Organic Matter.- 4.4.3 The Nutritional Value of Detrital Organic Matter (Detritus).- II: The Blueprint of the Model.- 5 The Construction of the Transport Submodel.- 5.1 Introduction.- 5.2 Diffusive Transport.- 5.2.1 Determination of the Constants.- 5.3 Transport of Particulate Material.- 5.3.1 Description.- 5.3.2 Vertical Transport Processes: Sedimentation and Resuspension.- 5.3.3 Horizontal Transport Processes.- 5.3.4 Boundary Conditions.- 5.3.5 Calibration of the Model.- 5.3.6 Detrital Carbon in the Mud.- 6 The Construction of the Pelagic Submodel.- 6.1 Introduction.- 6.2 Phytoplankton and Nutrients.- 6.2.1 State Variables.- 6.2.2 Irradiance and Photosynthesis.- 6.2.3 Nutrients.- 6.2.4 Assimilation.- 6.2.5 Loss Terms.- 6.3 Zooplankton.- 6.3.1 Microzooplankton.- 6.3.2 Mesozooplankton.- 6.3.3 Carnivorous Zooplankton.- 6.4 Pelagic Bacteria.- 6.4.1 Biomass.- 6.4.2 Uptake.- 6.4.3 Loss Terms.- 6.5 Oxygen in the Water.- 6.5.1 Physical and Chemical Aspects.- 6.5.2 Sources and Sinks of Oxygen.- 7 The Construction of the Benthic Submodel.- 7.1 Introduction.- 7.2 Benthic Primary Producers.- 7.2.1 Vertical Distribution of Biomass.- 7.2.2 Effects of Light.- 7.2.3 Specific Growth Rate and Primary Production.- 7.2.4 Excretion and Respiration.- 7.2.5 Suspension.- 7.3 Meiofauna.- 7.3.1 Food Uptake.- 7.3.2 Loss Factors.- 7.4 Macrobenthos.- 7.4.1 Biology.- 7.4.2 Model Description: Deposit Feeders.- 7.4.3 Model Description: Suspension Feeders.- 7.5 The Spatial Structure of the Sediment and Vertical Transport.- 7.5.1 Oxygen Demand and Sulphide Production.- 7.5.2 Nondiffusive Transport Processes.- 7.5.3 Diffusive Transport Processes.- 7.5.4 The Transition of Organic Matter Between the Benthic Layers.- 7.6 Benthic Bacteria.- 7.6.1 Distribution of Biomass.- 7.6.2 Uptake of Labile Organic Carbon.- 7.6.3 Detritus and Refractive Organic Matter.- 7.6.4 Mortality and Excretion.- 7.6.5 Respiration and Temperature Correction.- 7.6.6 Conclusion.- 8 The Construction of the Epibenthic Submodel.- 8.1 The State Variables.- 8.2 The Faunal Components of the Epibenthos.- 8.3 Migration.- 8.3.1 Redistribution.- 8.3.2 Comfort Functions.- 8.3.3 Immigration.- 8.3.4 Emigration.- 8.4 Uptake of Food.- 8.4.1 Calculation of Available Food.- 8.4.2 Uptake.- 8.5 Loss Factors.- 8.5.1 Respiration and Excretion.- 8.5.2 Mortality.- 8.6 Correction for Temperature.- 8.7 The Role of Foraging Birds.- 8.7.1 Estimation of the Number of Birds in the Ems Estuary.- 8.7.2 Calculation of Available Food for Birds.- 8.7.3 Uptake by Birds.- III: Results and Analysis.- 9 Running the Model.- 9.1 The Standard Run.- 9.2 The Initial Values of the State Variables.- 9.3 Validation of the Model.- 9.3.1 The Validation Sets.- 10 Results and Analysis of the Pelagic Submodel.- 10.1 Model Results and Validation of the Standing Stocks.- 10.1.1 Primary Producers.- 10.1.2 Microzooplankton.- 10.1.3 Mesozooplankton.- 10.1.4 Carnivorous Zooplankton.- 10.1.5 Pelagic Bacteria.- 10.1.6 Oxygen.- 10.1.7 Nutrients.- 10.1.8 The Detrital State Variables (PLOC, PDET, PROC, PDROC).- 10.2 Fluxes.- 10.2.1 Validated Fluxes.- 10.2.2 Nonvalidated Fluxes.- 10.3 Sensitivity Analysis.- 10.3.1 Degradation of Algal Production by Bacteria.- 10.3.2 Growth Efficiency of Bacteria.- 10.3.3 Suspended Phytobenthos as a Food Source for Zooplankton.- 10.3.4 The Role of Microzooplankton in the Model.- 10.3.5 Regulation of the Phytoplankton Succession.- 10.4 Conclusions.- 11 Results and Analysis of the Benthic Submodel.- 11.1 The Seasonal Cycle of the State Variables.- 11.1.1 Total and Anaerobic Bacterial Biomass.- 11.1.2 Phytobenthos.- 11.1.3 Meiobenthos.- 11.1.4 Macrobenthos.- 11.1.5 Organic Matter.- 11.1.6 Sulphide and Pyrite.- 11.1.7 The Location of the Sulphide Horizon.- 11.2 The Fluxes from and to the State Variables.- 11.2.1 Validated Fluxes.- 11.3 Unvalidated Fluxes.- 11.3.1 Diet of Meiofauna.- 11.3.2 Grazing and Predation in the Benthos.- 11.3.3 Carbon Budgets of Organisms.- 11.3.4 Net Production and Productivity.- 11.3.5 Dynamics of Refractory Organic Carbon in the Sediment.- 11.4 Sensitivity Analysis of the Benthic Subsystem.- 11.4.1 Reduced Detritus.- 11.4.2 Bacterial Excretion and Efficiency.- 11.4.3 Phytobenthos Regulation.- 11.4.4 The Role of Meiobenthos in the Benthic Community.- 11.4.5 The Activity Pattern of Macrobenthos.- 11.5 Conclusions.- 12 Results and Analysis of the Epibenthos Submodel.- 12.1 Model Results.- 12.1.1 The Standing Stocks in the Five Compartments.- 12.1.2 Internal Fluxes and Productivity.- 12.1.3 Carbon Fluxes to the Epibenthic Submodel.- 12.2 Sensitivity Analysis.- 12.2.1 Varying the Immigrating Biomass.- 12.2.2 Model Runs, Partially or Wholly Excluding Epibenthos.- 12.3 Conclusions.- 13 Results and Validation of the Transport Submodel.- 13.1 Introduction.- 13.2 Transport of Dissolved Compounds.- 13.2.1 Salinity.- 13.2.2 Dissolved Organic Carbon.- 13.3 Transport of Particulate Compounds.- 13.3.1 Suspended Sediment.- 13.3.2 Particulate Organic Carbon.- 13.3.3 Suspended Matter.- 13.4 Flows and Annual Budgets.- 13.4.1 Suspended Sediment Transport.- 13.4.2 Organic Carbon Transport.- 13.5 Sensitivity Analysis.- 13.5.1 Behaviour of Particulate Matter During Transport.- 13.5.2 The Role of Imported POC in the System.- 13.5.3 The Role of Silt in the Estuary.- 13.6 Conclusions.- 14 Model Applications and Limitations.- 14.1 Introduction.- 14.2 Limitations of the Model.- 14.2.1 Category I: “Physiological” Parameters.- 14.2.2 Category II: “Structural” Parameters.- 14.2.3 Category III: “Dimensional“ Parameters.- 14.3 Applications of the Model.- 14.3.1 Case 1: Reduced Organic Loading.- 14.3.2 Case 2: Applying the Ems Model to the Severn Estuary.- 14.4 Conclusions.- 15 References.- Appendix A: Parameter Descriptions and Values.- A-1: Parameters of the Physical Submodel.- A-2: Parameters of the Pelagic Submodel.- A-3: Parameters of the Benthic Submodel.- A-4: Parameters of the Epibenthic Submodel.- Appendix B: The FORTRAN Listing of the Submodels.- B-1: Subroutine BAHBOE.- B-2: Subroutine SUBPEL.- B-3: Subroutine SUBBEN.- B-4: Subroutine SUBEPI.- Appendix C: Data Files.- C-1: Data of the Physical Model.- C-2: Data of the Pelagic Model.- C-3: Data of the Benthic Model.- C-4: Data of the Epibenthic Model.- C-5: The Initial Values of the State Variables.