BioGeoChemical Processes in the Bay

Contributed by Jiangtao Xu and Raleigh Hood
University of Maryland Center for Environmental Science, Horn Point Laboratory.


The Xu/Hood (XH) biogeochemical model is a relatively simple NPZD-type water quality model that has been implemented online in a 3-dimensional, hydrodynamic/ circulation model of Chesapeake Bay by Jiangtao Xu and Raleigh Hood at the University of Maryland Center for Environmental Science. This simplified water quality model uses nitrogen as a currency but also includes a simple parameterization of phosphorus limitation. It predicts phytoplankton biomass/primary productivity, respiration and both organic and inorganic nutrient and particle concentrations. Dissolved oxygen concentration is also determined, light attenuation parameters are calculated, and a simple benthic biogeochemical model has been implemented.

The XH model consists of 3 primary components: 1) A 3-dimensional hydrodynamic model (Curvilinear Hydrodynamics in 3-Dimensions, CH3D), developed by the US Army Corp of Engineers for the Chesapeake Bay Program; 2) An empirical bio-optical model; and 3) A water column/benthic biogeochemical model (Xu, 2005; Xu and Hood, in prep.). Additional details on each of these three model components are as follows:

  1. CH3D provides temperature and salinity structure and the 3-dimensional circulation and tracer transport for the XH model, where the latter runs online in the former. Online means that the biogeochemical model runs as a subroutine in CH3D, i.e., the biogeochemical calculations are made simultaneously while the physical model is advecting and diffusing the biogeochemical constituents in 3-dimensions. CH3D was developed by the US Army Corp of Engineers for use by the Chesapeake Bay Program as an environmental management tool. For details and related applications see Johnson et al. (1993); Johnson et al. (1995); Sheng (1987); Wang and Chapman (1995); Hood et al. (1999); Xu et al. (2002).
  2. The bio-optical model estimates the diffuse attenuation coefficient (Kpar) and light penetration in the water column as a function of chlorophyll, salinity (as a proxy for colored dissolved organic matter - CDOM) and TSS (total suspended sediment) concentrations. This model was derived empirically specifically for Chesapeake Bay by regressing measured Kpar values against measured salinity, chlorophyll-a, and TSS concentrations. It accounts for ~70% of the observed Kpar variability in the Bay in both wet and dry years. The version included here is composed of two equations that are applied for 0-15 and > 15 ppt salinity regimes. For details see Xu (2005) and Xu et al. (2005).
  3. The XH biogeochemical model is based upon Hood et al. (2001). This model was constructed to represent biogeochemical N cycling dominated by planktonic microbial processes. The prognostic state variables in this biogeochemical model include phytoplankton (P), heterotrophs (H), dissolved inorganic nitrogen (DIN), dissolved organic nitrogen (DON), total suspended sediments (TSS), and oxygen(O) concentrations, where the latter two state variables are specific to the Chesapeake Bay implementation. The Chesapeake Bay version also includes a simple parameterization of phosphorus limitation which involves specifying seasonally varying phosphorus concentrations in the Bay and a fixed half saturation constant for phosphorus uptake by phytoplankton in the model. Sediment biogeochemical processes are represented in the bottom-most layer of the physical model, where heterotrophic (H) processes consume organic detritus and oxygen. A simple parameterization of denitrification is also included. For details see Xu (2005).

The coupled XH model also includes a data assimilation routine that "nudges"the state variables in the upper reaches of the tributaries toward observed concentrations. This nudging scheme corrects for unaccounted for sources and sinks of organic and inorganic nitrogen (such as marshes and groundwater flows) and therefore insures that the tributary loadings are correct.



Hood, R.R., N.R. Bates, D.G. Capone, and D.B. Olson, Modeling the effect of nitrogen fixation on carbon and nitrogen fluxes at BATS, Deep-Sea Research, 2nd Special Issue on the U.S. JGOFS Time-Series Stations, 48, 1609-1648, 2001.

Hood, R.R., H.V. Wang, J.E. Purcell, E.D. Houde, and L.W. Harding, Jr., Modeling particles and pelagic organisms in Chesapeake Bay: Convergent features control plankton distributions, Journal of Geophysical Research, 104, 1223-1243, 1999.

Johnson, B.H., K.W. Kim, R.E. Heath, B.B. Hsieh, and H.L. Butler, Validation of a three-dimensional numerical hydrodynamic model of Chesapeake Bay, Journal of Hydraulic Engineering, 119, 2-20, 1993.

Johnson, B.H., H.V. Wang, and K.W. Kim, Can numerical estuarine models be driven at the estuary mouth, in ASCE Estuarine and Coastal Modeling, pp. 255-267, Am. Soc. of Civ. Eng., New York, 1995.

Sheng, Y.P., On modeling three-dimensional estuarine and marine hydrodynamics, in Three-Dimensional Models of Marine and Estuarine Dynamics, edited by J.C.J. Nihoul, and B.M. Jamart, pp. 35-54, Elsevier, Amsterdam, 1987.

Wang, H.V., and R.S. Chapman, Application of vertical turbulence closure schemes in the Chesapeake Bay circulation model - a comparative study, in ASCE Estuarine and Coastal Modeling, pp. 283-297, Am. Soc. of Civ. Eng., New York, 1995.

Xu, J., Modeling the physical, optical and biological properties of Chesapeake Bay. Ph.D dissertation. University of Maryland, College Park, 2005.

Xu, J., and R.R. Hood, Modeling biogeochemical cycles in Chesapeake Bay with a coupled physical-biological model, Coastal Shelf and Estuarine Science, In preparation.

Xu, J., R.R. Hood, and S.-Y. Chao (2005)A simple empirical optical model for simulating Kd variability in a partially mixed estuary, Estuaries, in review.

Downloadable Implementation of the model

The CBModel_95 tar file contains the fortran code and the data files needed to run the model for the year 1995. The other tar files forcing_96.tar contains just the data files for the 1996 simulation. Extract them to a directory with

tar -xvf CBModel_95.tar

Compile the fortran model with most any Fortan 77 compliant compiler. f77 ch3d_biowp.f Execution of program will read the input files and produce a simulation for the year. The descriptions of the many fort.* files can be found in the initial comments of the code ch3d_biowp.f.

tom gross April 2005