The soil is divided into several organic pools for carbon and nitrogen. Some of these pools are compulsory while others can optionally be switched on or off. The humus pool, CHumus and NHumus, one soil litter pool, CLitter1 and NLitter1, and the surface litter pool, CLitterSurface and NLitterSurface, are always present. If manure is simulated (see section External Inputs) the faeces pool, CFaeces and NFaeces, should be switched on (see switch Faeces pool). Optionally pools for dissolved organic matter may be included in the simulations (see switch Dissolved Organics). This option allows for vertical transport of organic matter of the soil profile.
Soil organisms, microbes, decompose the organic matter and their activity therefore accounts for the fluxes between different compartments in the soil. Microbial biomass can optionally be dynamically interacting with the soil organic matter (i.e. switch Microbes is turned on), and in this case a microbial biomass pool is formed, CMicrobes and NMicrobes. Microbes are decomposing litter, faeces and humus at different rates depending on how many micro organisms that participate in the decomposition process. Therefore different fractions of the microbial biomass are allocated to decompose the litter, faeces and humus pools (see Figure 5.2 below). Subsequently the micro organisms only decompose the carbon in the pool in which they are situated. On the other hand, if the microbial biomass is not explicitly simulated, the biomass is implicitly included in the litter, humus and faeces pools.
The microbial activity can be different in different pools. It is also possible to add an extra litter pool, CLitter2 and NLitter2, which can differ from litter pool 1 in microbial activity (see switch Litter pools) if the microbial biomass is explicitly simulated.