Simulating biogeochemistry

Using a primary species to represent the microbe

The microbe species can be represented by a primary species, and the reactant (such as CHCOO in Eq. (1)) as a kinetic species. The database that comes with the geochemistry module contains three such species, called Biomass1, Biomass2, Biomass3, but more can easily be added along the lines of:

    "Biomass1": {
      "elements": {},
      "radius": -1.5,
      "charge": 0.0,
      "molecular weight": 1.0
    },

Note that radius = -1.5, which means that the Debye-Huckel activity coefficient is always unity. Also note that in this case the molecular weight is set to 1g.mol. This is important to remember when setting kinetic rate constants.

The advantage of using a primary species to represent a microbe is the simplicity: a new species is added to the database, and the kinetic rate is defined appropriately (a worked example is found below). The main disadvantages are that microbe mortality cannot be represented and the kinetic rates cannot depend on the free molality of the kinetic species, only its total mole number (if these are important, a kinetic species must be used, as per the next section)

It is important to consider whether the reactant can accurately be treated as a kinetic species, or whether it is at equilibrium with the aqueous solution, in which case this method should not be used.

An example is found on the sulfate reducer page.

Using a kinetic species to represent the microbe

In this case, the reactants and products of the catalysed equation are treated as species in equilibrium with the aqueous solution, and the microbe is a kinetic species that the geochemistry code handles separately. It is more likely that this more accurately represents reality than the previous method.

To represent Eq. (1), the database could contain

    "methanogen": {
      "species": {
        "CH3COO-": -1.0,
        "H2O": -1.0,
        "CH4(aq)": 1.0,
        "HCO3-": 1.0
      },
      "molar volume": 1,
      "molecular weight": 1E9,
      "logk": [2.7272, 2.641, 2.699, 2.933, 3.28, 3.788, 4.336, 4.789]
    },

It is usually advantageous to place this in the mineral species section of the database, because microbes are often assumed to be immobile and have activity 1, just like minerals. Otherwise, they could be treated as redox couples.

Studying the above database entry reveals the following.

1. The reactants in the original Eq. (1) (CHCOO in this case) must be brought to the right-hand side of the equation. This has the interpretation that "when a methanogen reacts, it removes acetate and water to produce methane and biocarbonate", viz:

2. The molar volume and molecular weight are largely unimportant. Users should set reasonable numeric values, and keep those values in mind when defining the kinetic rates (below), since they impact the numeric values of the rate parameters. In most cases, only the intrinsic_rate_constant is impacted: see the mortality page for an example.

3. The equilibrium constants must be manually entered. These may be derived from the existing database entries, or the reaction balancing functionality of the geochemistry module may be used. Examples are presented on the sulfate reductions and arsenate reduction pages. In the current case, the database contains:

    "CH3COO-": {
      "species": {
        "HCO3-": 2.0,
        "H+": 1.0,
        "O2(aq)": -2.0
      },
      ...
      "logk": [160.6192, 146.7487, 130.6352, 115.8131, 100.9856, 89.0757, 79.0857, 70.4395]
    },
    "CH4(aq)": {
      "species": {
        "H2O": 1.0,
        "H+": 1.0,
        "HCO3-": 1.0,
        "O2(aq)": -2.0
      },
      ...
      "logk": [157.892, 144.108, 127.936, 112.88, 97.706, 85.288, 74.75, 65.65]
    },

Subtracting the second from the first yields Eq. (1) and the equilibrium constants. For instance is the first entry.

The advantage of using a kinetic species to represent a microbe is the flexibility, for instance, mortality can be represented as a kinetic rate (see the examples below). Moreover, in many cases, it is likely that the reactants and products of the catalysed equation are at equilibrium with the aqueous solution, making this approach more suitable than the former approach. The main disadvantage is the complexity of correctly entering the required information into the database.

The following microbes appear in the standard MOOSE geochemistry database, and more can be added using the procedure mentioned above:

• sulfate_reducer that catalyses the reaction CHCOO + SO HCO + HS. The sulfate_reducer appears in the mineral species list, and has a molecular volume of 1cm.g and a molar mass of g.mol.

• methanogen that catalyses the reaction CHCOO + HO CH(aq) + HCO. The methanogen appears in the mineral species list, and has a molecular volume of 1cm.g and a molar mass of g.mol.

• arsenate_reducer that catalyses the reaction Lactate + 2HAsO + 2HO CO + CHCOO + As(OH). The arsenate_reducer appears as a redox couple, with a radius of -1.5, meaning that its activity will always be unity, and its molar mass is set to 1g.mol.

The molar masses are definitely incorrect, but they are only important to remember when setting the kinetic rates. The examples below discuss this in detail.

The following are worked examples:

• Simulating mortality

• Sulfate reducer example

• Arsenate reducer example

• Zoning in an aquifer (a reactive-transport model)