Instructions for Modifying and Executing MEM III

Introducton
The zero-dimensional Marsh Equilibrium Model provides a beautiful example of how a salt marsh plant community  interacts with the physical environment to perpetuate that environment for the survival of the salt marsh (within limits).  Call it salt marsh Gaia if you will.  MEM III (rev. 9-5-11) is the successor to the Morris et al. model published in 2002.  New to MEM III is a more explicit treatment of belowground organic matter and the incorporation of the sediment cohort model SEMIDEC (Morris and Bowden 1986).  The online version allows users to perform sophisticated experiments (see the exercises page) and to simulate sedimentation and sediment organic matter profiles in any tidal marsh. 

References
Morris, J.T. and W.B. Bowden. 1986. A mechanistic, numerical model of sedimentation, mineralization, and decomposition for marsh sediments. Soil. Sci. Soc. Amer. J. 50:96-105.
Morris, J. T., and B. Haskin 1990. A 5-yr record of aerial primary production and stand characteristics of Spartina alterniflora. Ecol. 71: 2209-2217.
Morris, J. T., P. V. Sundareshwar, C. T. Nietch, B. Kjerfve, and D. R. Cahoon 2002. Responses of coastal wetlands to rising sea level. Ecol. 83: 2869-2877.
Morris, J.T. 2006. Competition among marsh macrophytes by means of geomorphological displacement in the intertidal zone. Estuarine and Coastal Shelf Science 69:395-402.
Morris, J.T. 2007. Ecological engineering in intertidal saltmarshes. Hydrobiologia 577:161-168.
Morris, J.T., Edwards, J., Crooks, S., Reyes, E. 2012. Assessment of Carbon Sequestration Potential in Coastal Wetlands. Pp 517-532.  In: Recarbonization of the Bioshpere: Ecosystem and Global Carbon Cycle.  R. Lal, K. Lorenz, R. Hüttl, B. U. Schneider, J. von Braun (eds). Springer.

Email comments/questions to morris@biol.sc.edu

Instructions   
Any combination of inputs may be entered in the appropriate input cell(s).  Click on the "Run Simulation" button and the model will output marsh elevation and other predicted time-series corresponding to the combination of inputs that are provided.  Key on "restore inputs" to return the inputs to default values corresponding to conditions in marshes at North Inlet, SC.The model can simulate two scenarios:  a mature marsh or, if you check the restoration option, a marsh restoration. Simulations of mature marsh assume that the inventory of carbon in the root zone has already stabilized, while simulations of a restoration assume that the starting point is an inorganic soil with no existing inventory of organic carbon.  Unless the “simulate restoration” option is checked, the default output shows graphic results of the mature marsh simulation.  Numerical data output is contained in tables that can be accessed at the bottom of the main screen.

Outputs
Biomass vs Elevation:  this is a graph of the biomass profile that is set by your choice of maximum biomass, minimum and maximum elevations.
• Depth vs Time:  this is the depth of the marsh surface below MHW over time. Note that the depth oscillates with a periodicity of 18.6 yr owing to the effect of the lunar nodal cycle.  You may eliminate the effects of the lunar nodel cycle by zeroing its amplitude.
• Organic Matter vs Depth:  this is the concentration of sediment organic matter (% of dry weight) vs sediment depth.  This is computed using sediment cohort theory (Morris and Bowden 1986).  This is a recent  addtion to MEM.  The organic matter profile that is ploted is not today's profile.  Rather, it is a forecast of the profile 100 yr into the future.   However, with the century level sea-level rise set to 100 x the current rate of sea level rise (now the default condition), and with the marsh elevation in equilibrium, you can simulate today's profile.  In other words, the default simulation is that of the last 100 yrs at North Inlet.
• Biomass vs Time:  this is the standing biomass of marsh vegetation over time

• MSL and Marsh Elevation vs Time:  The MSL trajectory is determined by your choice of the current rate of sea level rise and the century level sea level.  Marsh elevation is a prediction.
• Carbon Accretion vs Time:  this is the net annual accretion of carbon over time
• Numerical outputs:  The ‘Time Series” tab at the bottom of the page opens a table with 100 yrs of MSL and marsh elevations.  The 'Sed Profiles' tab opens a table of sediment depth profiles of soil organic matter and bulk density.  Closing either of these brower windows should return you to the model screen. 
Options
• Check the "Simulate Restoration" box to simulate a marsh restoration.
  Use my biomass depth profile” allows you to input your own values for the vertical distribution of biomass.  This is defined by maximum and minimum elevations (relative to NAVD88) and the maximum standing biomass  (see biological inputs).  Maximum biomass may be changed without checking this option, but you cannot modify the range unless this option is checked.
  Seasonal Biomass”, when checked, simulates the effect of seasonal variation of standing biomass on sedimentation.  The default (checked) assumes seasonality.  

Physical Inputs

• Start (year) – This is the start date.  This is important only to aline the simulation with the lunar nodal cycle. 

• Century Sea Level (cm) – This is the amount of sea-level rise that will occur 100 years into the future. 

• Mean High Water (cm) – This is the average mean high water level (MHW) relative to MSL.
• Mean Sea Level (cm) – This is the elevation of mean sea level relative to NAVD88 (should be close to zero).
• Initial Rate SLR (cm/yr) – Today’s rate of sea-level rise.
• Suspended Sed. Conc. (mg/liter) – The local annual mean concentration of suspended solids.  For North Inlet we have used the average concentrations in tidal creeks within the estuary.
• Initial Elevation (cm)   This is the elevation of the marsh surface relative to NAVD88.  If you set elevation to a value that is outside the vertical range of biomass then initial biomass will drop to zero.
Biological Inputs
  Max elevation is the elevation (cm) relative to NAVD88 that defines the upper vertical limit of the vegetation.  This is adjusted automatically when you change Mean High Water in the Physical Inputs section, unless you have checked the “Use my biomass depth profile” in the Options section.
 Min elevation is the elevation (cm) relative to NAVD88 that defines the lower limit of the vegetation.  Note that min elevation is often negative.  This also is adjusted automatically when you change Mean High Water in the Physical Inputs section, unless you have checked the “Use my biomass depth profile”.  
• Max peak biomass (g/m2) is the maximum end-of-year standing biomass at the optimum elevation
 OM decay rate (1/year) – This is the decay rate of labile sediment organic matter.
 Root&Rhizome:Shoot Ratio (g/g) This is the ratio of root and rhizome biomass to aboveground standing biomass.
kr (g/g) – The fraction of the belowground production that is eventually incorporated into stable soil carbon.
• BG turnover rate (1/year) – The turnover rate of belowground biomass.
• Max Root Depth (cm) - This is the depth in sediment above which 95% of live roots are found.  The root profile is assume to be a exponentially distributed with the maximum biomass at the sediment surface.
Original Model Inputs
ks (g-1m2yr-1) – This is the trapping efficiency or clearing rate of suspended particles by vegetation.  The default is based on North Inlet data.  This should be a universal constant, provided the energy environment and vegetation are like that of the North Inlet.   
q (yr-1) This is the net settling velocity or clearing rate of suspended particles in the absence of vegetation.  The default is based on North Inlet data.  This should be a universal constant, provided the energy environment is like that of a marsh platform with laminar flow.