Environment

Environment models

Models in the environment subproject consists in features defining the shape of the soil simulated by the Cammisol model, and C/N/P compartments.

C/N/P nutrients of the soil are distributed in several compartments. Each compartment is associated to a dynamic C/N/P quantity.

// TODO: include POM in SOM

• Soil Organic Matter (SOM): contains all organic matter components of the soil, in different forms. All compartments are represented as raw C/N/P quantities, as the exact chemical speciation of each component is assumed unknown.
  • Particular Organic Matter (POM): coarse organic matter that cannot be assimilated by microorganisms, but can be decomposed. Is it itself divided in two compartments.
    • Recalcitrant OM: big and complex macromolecules, such as lignin. Proteins and other N/P based nutrients are "trapped" in macro-molecules. This matter is hard (or even impossible) to decompose by microorganisms.
    • Labile OM: smaller organic compounds such as cellulose, sugars and simple proteins. Contrary to the recalcitrant OM, enzymes can target specific compounds in this compartment. The substrate can be attacked with enzymes produced by most microorganisms.
  • Dissolved Available Matter (DAM): contains all components assimilable by microorganisms. It is constituted by C/N/P components smaller than the labile OM. It contains products of the decomposition of the POM by microorganisms.
    • Dissolved Organic Matter (DOM): dissolved proteins, carboxylic acids and other assimilable polymers.
    • Dissolved Inorganic Matter (DIM): N and P in their inorganic forms (NH4, NO3, PO4)
  • Mineral Associated Matter (MAM): components associated to mineral phases due to the chemical adsorption of dissolved components (not yet implemented).
    • Mineral Associated Organic Matter (MAOM): organic matter associated to mineral.
    • Mineral Associated Inorganic Matter (MAIM): N and P ions associated to minerals (mostly P ions).

All those compartments are then spacialised in a 2D grid, that actually represents a volume of soil. Future iterations of the model plan to actually represent the 3D cube structure.

Each particle can be associated to a nutrient compartment:

• Black cubes representing PoreParticles, that contains the soil solution and microorganisms: DAM
• Green cubes representing OrganicParticles: POM
• Yellow cubes representing MineralParticles: MAM

Experiments

• File: models/cammisol/environment/grid.gaml
• Experiment: cammisol_environment

cammisol_environment

This experiment can be used to monitor the shape of the environment, and the initial repartition of C/N/P among the POM and the DAM.

Experiment parameters

Parameter	Description
Legend	Draws the legend of the grid

Grid parameters

Parameter	Description
Soil size	Length of the side of the square surface of soil represented by the grid (e.g. 1#m, 2#cm). The volume of soil represented by the model is thus equal to Soil size ^ 3.
Grid size	Number of cells on the side of the square grid representing the soil surface. This has no influence on the soil surface. For example, if Soil size equals 1#cm and Grid size is 10, then the grid contains 10*10=100 cells, each with a surface of 1#cm2/100 = 0.01#cm2.
Organic particle rate	Rate of OrganicParticles in the grid.
Mineral particle rate	Rate of MineralParticles in the grid.
Bulk density	Solid matter weight by volume of dry sol.

The grid is randomly built so that the probability of each cell to be an OrganicParticle or a Mineral Particle is equal to the corresponding rates, and the probability to be a Pore particle is thus 1 - Organic particle rate - Mineral particle rate.

POM parameters

Parameter	Description	Unit
C concentration in POM	Initial concentration of C in the particular organic matter.	Weight of C by weight of dry soil.
N concentration in POM	Initial concentration of N in the particular organic matter.	Weight of N by weight of dry soil.
P concentration in POM	Initial concentration of P in the particular organic matter.	Weight of P by weight of dry soil.
Rate of labile OM in POM	Rate of OM that is considered as labile OM to initialise the POM. The rest is considered as recalcitrant OM.

Each PoreParticle contains an initially empty DAM. Each PoreParticle also embeds an initially empty OrganicParticle, that might contain necromass and residual POM. The total quantities of C/N/P in the POM can be easily computed as soil volume * bulk density * C/N/P concentration in POM. Those quantities are then equally distributed among all OrganicParticles, except OrganicParticles embedded in PoreParticles. More precisely, a rate of labile_rate is added to each C/N/P_labile section of OrganicParticles, and the rest is added to C/N/P_recalcitrant.

DAM parameters

Parameter	Description	Unit
C concentration in DOM	Initial concentration of C in the dissolved organic matter.	Weight of C by weight of dry soil.
N concentration in DOM	Initial concentration of N in the dissolved organic matter.	Weight of N by weight of dry soil.
P concentration in DOM	Initial concentration of P in the dissolved organic matter.	Weight of P by weight of dry soil.
N concentration in DIM	Initial concentration of N in the dissolved inorganic matter.	Weight of N by weight of dry soil.
P concentration in DIM	Initial concentration of P in the dissolved inorganic matter.	Weight of P by weight of dry soil.

DOMs and DIMs in each DAM are initialised similarly to OrganicParticles, from the provided concentrations.

Default outputs

Grid

C compartments

N compartments

P compartments