The soil model#

Model overview#

The soil model comprises of a number of carbon, nitrogen and phosphorus pools. These pools are updated by numerical integration, of the following set of processes:

  1. Soil receives inputs from litter decay and the decay of animal necromass (simulated within the animal model). These inputs are split into dissolved and particulate forms, and the nutrient content is further divided into organic and inorganic forms.

  2. Carbon is transformed between two different protected forms and a form usable by microbes. The rates at which this happens is based on environmental conditions and presence of microbially produced enzymes in the soil.

  3. Microbes grow by taking up carbon, nitrogen and phosphorus from the soil. Some of the carbon that microbes uptake is respired in order to gain energy, this carbon is then lost to the soil.

  4. Mycorrhizal fungi are a special case of microbial nutrient uptake, as they are entirely dependent on their host plant for carbon. They uptake nitrogen and phosphorus (in both organic and inorganic forms), some of which is used for growth and maintenance, with the rest being supplied to their symbiotic plant partners.

  5. Fungi allocate a certain proportion of their growth to the production of reproductive fruiting bodies. These bodies are either consumed by animals or decay back into the soil.

  6. While organic nutrient flows follow the flow of carbon, nutrient cycling also involves inorganic nutrients which cycle independently. These cycles couple due to microbial mineralisation, which in our model occurs when microbes have an excess of nutrients and so release them in an inorganic form.

  7. Inorganic nitrogen can also be formed through nitrogen fixation. Our model includes both plant-associated and free-living versions of this process.

  8. This nitrogen, which is fixed in the form of ammonium, can nitrify to form nitrate, another inorganic form of nitrogen that both plants and microbes can utilise. This nitrate can be denitrified which causes the nitrogen contained in it to be lost from the soil.

  9. Labile inorganic phosphorus can also be released from mineral forms in the soil. This labile inorganic phosphorus can be used by both plants and microbes, but can become inaccessible when it associates with soil minerals.

  10. Many nutrients forms are also soluble, these can then be lost from the soil due to nutrient leaching.

  11. The soil model also allows animals to consume POM, soil bacteria and soil fungi.

The model contains four functional groups (bacteria, saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi). Similarly, enzyme classes are distinguished by whether they were produced by fungi or bacteria and by what substrate they break down (MAOM or POM). So, there is a total of four enzyme classes in the model.

If you want to understand the model flow in greater detail, please consult the soil model API documentation.

Model variables#

There are five different relationships that models can have with variables. The links in the list below provide summaries of all variables the soil model has each specific relationship with: