Toolbox: community

A collection of routines for interacting populations in an environment with nutrient recycling

mixo

A one-species community of mixotrophs: organisms that can assimilate according to the phototrophic route (light plus inorganic carbon and nutrients), and the heterotrophic route (digestion of organic carbon, in this case dead individuals). Demo that runs: The theory for the model can be found in:
Kooijman, S. A. L. M., Dijkstra, H. A. and Kooi, B. W. 2002 Light-induced mass turnover in a mono-species community of mixotrophs. J. Theor. Biol. 214: 233 - 254.
The paper describes how light affect the turnover rates of organic matter and nutrients in a community that is open for energy, but closed for mass. It also deals with steady states as functions of light, total carbon and total nitrogen, and depth-profiles of systems' components, including the ratio of the auto versus heterotrophic activities.

Example of use: mixo


shtime*_mixo

Ontogeny of a batch reactor of mixotrops with * reserves, where * = 0, 1, or 3. Initial conditions can be changed by editing the files pars0_mixo.m, pars1_mixo.m or pars3_mixo.m.
The figures show all the state variables against time.

Example of use after editing pars*_mixo.m for * = 0, 1 or 3: shtime*_mixo. The command shtime1_mixo (4) will only plot fig 4 of the mixotroph community with 1 reserve.


shstate*_mixo

Equilibrium of a batch reactor of mixotrops with * reserves, where * = 0, 1, or 3 as functions of light, total carbon and total nitrogen. The maximum values of these three system parameters are set in pars*_mixo.m.

The distribution of carbon and nitrogen over the compounts are plotted cumulatively, so they sum to fixed totals.
For carbon from bottom to top: DIC, structure-detritus, reserve-detritus (for * = 1, 3), structure, reserve (for * = 1, 3), carbon-reserve (for * = 3). The curves between the type of detritus, and between structure and reserves are stippled.
For nitrogen from bottom to top: DIN, structure-detritus, reserve-detritus (for * = 1, 3), structure, reserve (for * = 1, 3), nitrogen-reserve (for * = 3). The curves between the type of detritus, and between structure and reserves are stippled.

Two equilibria can exist for the 3-reserve model. If this happens, both branches are shown; one branch is plotted in magenta.

Example of use after editing pars*_mixo.m for * = 0, 1 or 3: shstate*_mixo. The command shstate1_mixo (2) will only plot fig 2 of the mixotroph community with 1 reserve.


shgrad*_mixo

Shows gradients of mixotrops with * reserves, where * = 0, 1, or 3 as function of depth. The parameters are set in pars*_mixo.m. The number of layers is set in shgrad*_mixo; the light intensity reduces by a fixed factor between subsequent layers; this factor is set in pars*. The upward and downward specific mixing rates can be set per state variable (but make sure that that for structure and reserves are equal).

The output represent the state variables (in the columns) for the different layers (in the rows; the first row represents the surface layer) at the last time point of integration (set by tmax in shgrad*).

If a plot number is specified, the gradient ontogeny is shown, starting from a homogeneous distribution. The stack of layers is closed for mass (no downward transport). If no plot number is specified, all state variables as plotted as a function of depth for the last time point only.

Example of use after editing pars*.m for * = 0, 1 or 3: X = shgrad*_mixo;. The command X = shgrad1_mixo (2) will show a movie for state variable 2 (which is DIN) as a function of depth during time with 1 reserve; it also prints the final gradient.


Back to the DEBtool page