6.11. jules_soil_biogeochem.nml

This file sets options and parameters for soil biogeochemistry.

If using the single-pool or 4-pool soil models, all soil parameters are read from this file.

If using the ECOSSE soil model, most soil parameters are read from a separate file (jules_soil_ecosse.nml).

6.11.1. JULES_SOIL_BIOGEOCHEM namelist members

JULES_SOIL_BIOGEOCHEM::soil_bgc_model

Type:

integer

Permitted:

1, 2 or 3

Default:

1

Choice for model of soil biogeochemistry.

Possible values are:

1. A single-pool model of soil carbon turnover in which the pool is not prognostic (not updated).

   This must be used when the TRIFFID vegetation model is not selected (l_triffid = FALSE).
2. A 4-pool model of soil organic carbon and nitrogen, originally based on the Jenkinson (1990) model, with a single pool of inorganic N.

   Historically this was bundled with the TRIFFID vegetation model.

   This can only be used if the TRIFFID vegetation model is selected (l_triffid = TRUE).
3. A 4-pool model of soil organic carbon and nitrogen, and 2 inorganic N pools (ammonium and nitrate), based on the ECOSSE model (Smith et al., 2010).

   This can only be used if the TRIFFID vegetation model is selected (l_triffid = TRUE).

   This can also be run without nitrogen (l_soil_n = FALSE).

Warning

The ECOSSE model in JULES is still in development and is not fully functional in this version. The code is included to allow further development. Users should not try to use ECOSSE.

See also

References:

• Jenkinson, D.S., 1990. The turnover of organic carbon and nitrogen in soil. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 329(1255), pp.361-368. (https://doi.org/10.1098/rstb.1990.0177)

• Smith et al., 2010, Estimating changes in Scottish soil carbon stocks using ECOSSE. I. Model description and uncertainties, Climate Research, 45: 179-192. (https://doi.org/10.3354/cr00899).

Parameters that can be used with all soil models

JULES_SOIL_BIOGEOCHEM::q10_soil

Type:

real

Default:

2.0

Q10 factor for soil respiration.

With the single-pool or 4-pool models this is only used if l_q10 = TRUE.

With the ECOSSE model this is only used if temp_modifier = 1.

See Hadley Centre Technical Note 24, Eq.17, available from the Met Office Library.

Parameters for the single-pool model (only used if soil_bgc_model = 1)

JULES_SOIL_BIOGEOCHEM::kaps

Type:

real

Default:

0.5e-8

Specific soil respiration rate at 25 degC and optimum soil moisture (s^-1).

See Hadley Centre Technical Note 24, Eq.16, available from the Met Office Library.

Parameters for the single-pool and 4-pool models (only used if soil_bgc_model = 1 or 2)

JULES_SOIL_BIOGEOCHEM::l_q10

Type:

logical

Default:

T

Switch for use of Q10 approach when calculating soil respiration.

TRUE

Use Q10 approach (Equation 65 in Clark et al., 2011).

Note

This is always enforced if the single-pool model is selected (soil_bgc_model = 1) and was used in JULES2.0.

FALSE

Use the approach of Jenkinson (1990) (Equation 66 in Clark et al., 2011).

See also

References:

• Jenkinson, D.S., 1990. The turnover of organic carbon and nitrogen in soil. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 329(1255), pp.361-368. (https://doi.org/10.1098/rstb.1990.0177)

• Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description – Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701–722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.

JULES_SOIL_BIOGEOCHEM::l_soil_resp_lev2

Type:

logical

Default:

F

Switch affecting the temperature and moisture used for soil respiration calculation.

TRUE

Temperature and total (frozen+unfrozen) moisture content of the second soil layer are used.

FALSE

Temperature and unfrozen moisture content of the first (topmost) soil layer are used.

Note

If layered soil C is used (l_layeredc = TRUE) the temperature and moisture of each soil layer is used to calculation respiration from that layer.

Parameters for the 4-pool model (only used if soil_bgc_model = 2)

JULES_SOIL_BIOGEOCHEM::l_layeredc

Type:

logical

Default:

F

Switch for using the layered soil carbon model.

If the 4-pool model is used (soil_bgc_model = 2) this uses the approach of Burke et al. (2017) and two extra parameters are required: tau_resp, tau_lit.

Layered soil nitrogen is also available if the nitrogen cycle is switched on (l_nitrogen = TRUE), but this is a highly experimental version which needs further evaluation and so should be used with extreme caution. One additional parameter is required for layered soil nitrogen: diff_n_pft.

TRUE

The number and thickness of layers in the soil carbon model are set equal to those in the soil moisture model (JULES_SOIL).

FALSE

There are no specific layers in the soil carbon model (a single, bulk pool).

See also

References:

• Burke, E. J., Chadburn, S. E., and Ekici, A.: A vertical representation of soil carbon in the JULES land surface scheme (vn4.3_permafrost) with a focus on permafrost regions, Geosci. Model Dev., 10, 959-975, doi:10.5194/gmd-10-959-2017, 2017.

JULES_SOIL_BIOGEOCHEM::l_label_frac_cs

Type:

logical

Default:

F

Switch for labelling and tracing a subset of the layered soil carbon (l_layeredc = TRUE). It uses the approach of Burke et al.(2017). This requires the 4-pool model to be used (soil_bgc_model = 2). The fraction of labelled soil carbon needs to be specified as part of the model’s initial state.

TRUE

A user-defined fraction of soil carbon is labelled.

FALSE

None of the soil carbon is labelled.

See also

References:

• Burke, E. J., Chadburn, S. E., and Ekici, A.: A vertical representation of soil carbon in the JULES land surface scheme (vn4.3_permafrost) with a focus on permafrost regions, Geosci. Model Dev., 10, 959-975, doi:10.5194/gmd-10-959-2017, 2017.

JULES_SOIL_BIOGEOCHEM::kaps_4pool

Type:

real(4)

Default:

3.22e-7, 9.65e-9, 2.12e-8, 6.43e-10

Specific soil respiration rate for the 4-pool submodel for each soil carbon pool (decomposable plant material, resistant plant material, biomass, humus).

JULES_SOIL_BIOGEOCHEM::bio_hum_cn

Type:

real

Default:

10.0

Parameter controlling ratio of C to N for BIO and HUM pools.

JULES_SOIL_BIOGEOCHEM::sorp

Type:

real

Default:

10.0

Parameter controlling the leaching of inorganic N through the soil profile. A factor of 1 means that in a timestep all the inorganic N is available for leaching. The default value of 10 means that 10% of inorganic N is available for leaching.

JULES_SOIL_BIOGEOCHEM::n_inorg_turnover

Type:

real

Default:

1.0

Parameter controlling the lifetime of the inorganic N pool. A value of 1 implies the whole pool will turnover in 360 days.

JULES_SOIL_BIOGEOCHEM::tau_resp

Type:

real

Default:

2.0

Parameter controlling decay of respiration with depth (m-1). Only used with layered soil carbon (l_layeredc = TRUE).

JULES_SOIL_BIOGEOCHEM::diff_n_pft

Type:

real

Default:

5.0

Parameter controlling the rate of re-filling of the available inorganic nitrogen pool (1/360 days). This parameter determines how quickly the inorganic nitrogen reaches the roots after the roots uptake from the soil around them. This should be quicker than the turnover rate of inorganic nitrogen. In addition, it has to be small compared with the triffid timestep (360/triffid_period) otherwise the available inorganic nitrogen becomes unstable. Hence the choice of the default value 5. Only used with layered soil carbon and nitrogen scheme (l_layeredc = TRUE and l_nitrogen = TRUE). When l_trif_eq = TRUE or diff_n_pft is greater than (0.5 * 360 / triffid_period) then all of the inorganic nitrogen pool is deemed to be available.

JULES_SOIL_BIOGEOCHEM::z_burn_max

Type:

real

Default:

0.2

Parameter controlling the depth to which fire burns soil litter carbon in metres. At depths shallower than this value, the fire can burn soil carbon in the two litter pools (dpm and rpm). If z_burn_max falls within a layer only a proportion of the soil carbon is burnt. Only used with layered soil carbon scheme (l_layeredc = TRUE) and fire (either l_trif_fire or l_inferno or both). In reality the burn depth varies so please check whether the default value of 0.2 is suitable for your application.

Parameters for the 4-pool- or ECOSSE-based models (only used if soil_bgc_model = 2 or 3):

JULES_SOIL_BIOGEOCHEM::tau_lit

Type:

real

Default:

5.0

Parameter controlling the decay of litter with depth (m-1). With 4-pool, this is only used with layered soil carbon (l_layeredc = TRUE). With ECOSSE, this is only used with plant_input_profile = 2.

Methane parameters and switches. Can only be used with the single-pool and 4-pool models (soil_bgc_model = 1 or 2).

Warning

Some parameters may need to be re-tuned for different soil biogeochemistry models.

JULES_SOIL_BIOGEOCHEM::l_ch4_tlayered

Type:

logical

Default:

F

Switch to calculate methane emissions based on layered soil temperature.

TRUE

Methane emission is calculated from layered soil temperatures.

FALSE

Methane emission is calculated from top 1m average soil temperature (default).

JULES_SOIL_BIOGEOCHEM::l_ch4_interactive

Type:

logical

Default:

F

Switch to couple the methane emission into the carbon cycle. In order to use this the methane must be calculated from layered soil temperature (l_ch4_tlayered = TRUE).

TRUE

Methane flux is subtracted from soil carbon stocks.

FALSE

Methane emission is only diagnostic (default).

JULES_SOIL_BIOGEOCHEM::l_ch4_microbe

Type:

logical

Default:

F

Switch to enable the microbial methane production scheme (represents the dynamics of methanogens and a dissolved substrate pool). See Chadburn et al. (2020).

Note

This will only be applied to the methane production from your chosen ch4_substrate. The scheme has been calibrated with ch4_substrate = 1.

TRUE

Microbial dynamics simulated in methane scheme.

FALSE

No microbial dynamics, decomposition of substrate translates immediately to methane emissions.

JULES_SOIL_BIOGEOCHEM::ch4_substrate

Type:

integer

Permitted:

1, 2 or 3

Default:

1

Choice of substrate for wetland methane. This controls the calculation method for the methane flux that is used to update soil carbon (only if l_ch4_interactive = TRUE) and to populate the variable fch4_wetl (seen by the atmospheric model in coupled mode).

Possible values are:

1. Using soil carbon as substrate (default).
2. Using NPP as substrate.
3. Using soil respiration as substrate.

This replaces the previous switch l_wetland_ch4_npp.

JULES_SOIL_BIOGEOCHEM::t0_ch4

Type:

real

Default:

273.15

Reference temperature for the Q10 function CH4 emission calculation

JULES_SOIL_BIOGEOCHEM::const_ch4_cs

Type:

real

Default:

7.41e-12

Scale factor for wetland CH4 emissions when soil carbon is taken as the substrate for ch4 emissions (ch4_substrate = 1)

Note

In the UM the recommended value depends on l_triffid as follows:

l_triffid = FALSE, const_ch4_cs = 5.41e-12

l_triffid = TRUE, const_ch4_cs = 5.41e-10

JULES_SOIL_BIOGEOCHEM::q10_ch4_cs

Type:

real

Default:

3.7

Q10 value for wetland CH4 emissions when soil carbon is taken as the substrate for ch4 emissions (ch4_substrate = 1)

JULES_SOIL_BIOGEOCHEM::const_ch4_npp

Type:

real

Default:

9.99e-3

Scale factor for wetland CH4 emissions when NPP is taken as the substrate for ch4 emissions (ch4_substrate = 2)

JULES_SOIL_BIOGEOCHEM::q10_ch4_npp

Type:

real

Default:

1.5

Q10 value for wetland CH4 emissions when npp is taken as the substrate for ch4 emissions (ch4_substrate = 2)

JULES_SOIL_BIOGEOCHEM::const_ch4_resps

Type:

real

Default:

4.36e-3

Scale factor for wetland CH4 emissions when soil respiration is taken as the substrate for ch4 emissions (ch4_substrate = 3)

JULES_SOIL_BIOGEOCHEM::q10_ch4_resps

Type:

real

Default:

1.5

Q10 value for wetland CH4 emissions when soil respiration is taken as the substrate for ch4 emissions (ch4_substrate = 3)

JULES_SOIL_BIOGEOCHEM::ch4_cpow

Type:

real

Default:

1.0

Power of soil carbon used to calculate methane emissions with soil carbon as substrate (ch4_substrate = 1). Methane production is calculated as cs^ch4_cpow. A value of 1.0 is default, but a value of 2/3 is consistent with an assumption that only the surfaces of the organic matter are accessible.

Note

const_ch4_cs will need retuning if this parameter is changed.

Methane parameters only used with layered soil temperatures (l_ch4_tlayered = TRUE).

JULES_SOIL_BIOGEOCHEM::tau_ch4

Type:

real

Default:

6.5

Exponent in the exponential decline of methane emissions with soil depth (m-1). This empirically represents methane oxidation/emission processes, which only allow a fraction of the methane produced in the soil to reach the atmosphere.

Methane parameters only used with microbial methane scheme (l_ch4_microbe = TRUE).

JULES_SOIL_BIOGEOCHEM::k2_ch4

Type:

real

Default:

0.01

Baseline methanogenic respiration rate (hr-1).

JULES_SOIL_BIOGEOCHEM::kd_ch4

Type:

real

Default:

0.0003

Baseline methanogenic mortality rate (hr-1).

JULES_SOIL_BIOGEOCHEM::rho_ch4

Type:

real

Default:

47.0

Factor in substrate limitation function (related to half saturation of substrate for methanogenic respiration) ( (mgC/m3)-1 ).

JULES_SOIL_BIOGEOCHEM::q10_mic_ch4

Type:

real

Default:

4.3

Q10 factor for methanogens.

JULES_SOIL_BIOGEOCHEM::cue_ch4

Type:

real

Default:

0.03

Carbon use efficiency of methanogenic growth.

JULES_SOIL_BIOGEOCHEM::mu_ch4

Type:

real

Default:

0.00042

Threshold growth rate below which methanogens die (hr-1).

JULES_SOIL_BIOGEOCHEM::frz_ch4

Type:

real

Default:

0.5

Factor to reduce CH4 substrate production when soil is sufficiently frozen (only in microbial scheme).

JULES_SOIL_BIOGEOCHEM::alpha_ch4

Type:

real

Default:

0.001

Ratio between maintenance and growth respiration rates for methanogens.

JULES_SOIL_BIOGEOCHEM::ev_ch4

Type:

real

Default:

5.0

Timescale over which methanogenic traits adapt to temperature change (yr)

JULES_SOIL_BIOGEOCHEM::q10_ev_ch4

Type:

real

Default:

2.2

Q10 for temperature response of methanogenic traits under adaptation

See also

Reference for microbial methane scheme:

• Chadburn, S. E. et al (2020), Modeled Microbial Dynamics Explain the Apparent Temperature Sensitivity of Wetland Methane Emissions. Global Biogeochemical Cycles, 34: e2020GB006678. https://doi.org/10.1029/2020GB006678