To assess the soil quality of an agricultural field, soil properties
are used to derive so-called soil functions. Theses soil functions
represent distinct processes in soil supporting the sustainable crop
development. In this section the available soil functions are presented
and illustrated.
General supporting soil properties
Since the quality of a soil is evaluated given its crop rotation
plan, soil type, and geohydrological conditions, a few general
derivative soil properties are estimated. These include the calculation
of bulk density, rooting depth, organic carbon stocks, the age of
grassland, and the fraction that a crop contributes to the crop rotation
plan. These general properties are explained below.
Estimate bulk density
Soil Bulk density is estimated via a pedotransferfunction using
‘calc_bulk_density’ currently used in Dutch fertilizer recommendation
systems. It requires as input the agronomic soil type, the soil organic
matter content, and the clay content of the topsoil analyzed. For
details see ?calc_bulk_density. Generally, the bulk density
declines with the soil organic matter level in the soil and is higher in
sandy soils compared to clayey soils.
Estimate other general properties
Agricultural soils are frequently analyzed in routine agricultural
laboratories. In the Netherlands the soil layer analyzed, is the top
25cm of an arable soil and the first 10 cm of a grassland soil. To
convert soil nutrient concentrations (mg / kg) to a hectare basis, one
need to know the soil depth analyzed. The OBIC function for this is a
rather simple one, calc_root_depth where the details can be
found via ?calc_root_depth. The only input required is the
crop code.
The Carbon pool in soil (kg / ha) is subsequently calculated from the
soil organic matter content, the bulk density, and the sample depth via
calc_organic_carbon. For details, see
?calc_organic_carbon.
The age of grassland is calculated via the function
calc_grass_age given the series of crop codes available per
field. These crop codes have a temporal order with the most recent ones
on top. For details, see ?calc_grass_age.
Lastly, the relative contribution of a few crops to the full crop
rotation plan over the last ten years can be estimated via the function
calc_rotation_fraction. This function has as input the
field-ID, the series of crop codes and the name of the crop for which
one likes to know the relative fraction within a crop rotation plan. The
following options are possible: starch, potato, sugarbeet, grass, mais,
alfalfa, catchcrop, cereal, clover, nature, rapeseed, other, rustgewas,
and rustgewasdiep.
An example of these functions is illustrated below.
# estimate soil bulk density
dt[, D_BDS := calc_bulk_density(B_SOILTYPE_AGR, A_SOM_LOI, A_CLAY_MI)]
# estimate soil sampling depth
dt[, D_RD := calc_root_depth(dt$B_LU_BRP)]
# estimate Carbon pool
dt[, D_OC := calc_organic_carbon(A_SOM_LOI, D_BDS, D_RD)]
# estimate age of grassland
dt[,D_GA := calc_grass_age(ID, B_LU_BRP)]
# estimate crop rotation fraction for sugar beet
dt[, D_CP_SUGARBEET := calc_rotation_fraction(ID, B_LU_BRP, crop = "sugarbeet")]
Calculate series of chemical soil functions
The open soil index quantifies and evaluates the capacity of the soil
to supply nitrogen, phosphorus, potassium, magnesium, copper, and zinc
as well as the capacity of the soil to buffer cations and the pH. The
different functions are illustrated and explained below.
Nitrogen supplying capacity
Nitrogen is the nutrient that plants need most and is often the first
limiting factor for growth. Plants take up nitrogen in mineral form as
nitrate and ammonium. However, nitrogen is largely present in the soil
in organic compounds. The availability of N to plants during the growing
season therefore depends on the extent and rate of mineralization from
the organic matter.
Nitrogen supply on grassland is derived from empirical datasets
relating total N levels in soil to the N supply, depending on sampling
depth, soil texture, and the age of the grassland. For arable fields,
the N supply is derived from a simple first order decomposition model,
calibrated for Dutch circumstances and depending on soil texture,
organic matter, and total N content.
To estimate the N supplying capacity of the soil, one can make use of
the function calc_nlv. For more details, see
?calc_nlv.
# estimate nitrogen supply (kg N / ha)
dt[, D_NLV := calc_nlv(B_LU_BRP, B_SOILTYPE_AGR, A_N_RT, A_CN_FR, D_OC, D_BDS, D_GA)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
total N and NLV for a grassland soil. In summary, the N supplying
capacity of a soil increases with the total N present in the soil.
The total N supply is evaluated via a parabolic scoring function with
an optimum of 100 kg N / ha in arable fields and 140 kg N / ha in
grassland fields. The conversion from N supply to an index representing
the distance to target is further explained in section
Phosphorus Availability Index
Phosphate (P) is present in the soil in both inorganic and organic.
Inorganic P present in the soil solution is directly available for plant
uptake. The amount of P in the soil solution is small compared to the
total P supply of the soil. Organic P is only available to the plant
after decomposition by micro-organisms. The undissolved inorganic and
organic P compounds can be divided into labile and stable compounds:
- The labile P fraction is in equilibrium with the P in solution and
is the main source of P re-supply to the soil solution. Labile inorganic
P compounds include P bound to the surface of iron and aluminium (hydr-)
oxides, and iron (Fe), aluminium (Al) and calcium phosphates. In acid
and neutral soils, P availability is mainly determined by its binding to
Fe and Al (hydr-) oxides. In calcareous soils, P is usually associated
with calcium (Ca).
- The stable P compounds are usually poorly soluble and therefore
poorly available to plants. Stable inorganic P compounds include
P-containing soil minerals (e.g. apatite).
The phosphorus supply of an agricultural soil can be derived from
methods measuring either a capacity or an intensity of P pools in soil
or a combination of both. The latter approach is followed for grassland
and maize fields, where the optimum P supply is derived from multiple
field experiments across the Netherlands. For arable farming systems,
the phosphorus supply is derived from one measured P pool reflecting the
P status as well as controlling the crop response to P inputs. The
availability is highly controlled by chemical adsorption and desorption
equilibria and affected by the iron and aluminum oxides content of soils
as well as the availability of oxygen. A phosphorus supply around 4.8
(unitless index, for maize and grassland fields) and 45 (mg P2O5 per
liter, for arable fields) is optimal for crop production.
To estimate the P availability of the soil, one can make use of the
function calc_phosphate_availability. The function requires
the following input: the BRP crop code and P concentration P measured
via extraction of ammonium lactate (A_P_AL), water (A_P_WA) or 0.01M
CaCl2 (A_P_CC).
For more details, see ?calc_phosphate_availability.
# estimate phosphate availability index (unitless)
dt[, D_PBI := calc_phosphate_availability(B_LU_BRP, A_P_AL, A_P_CC, A_P_WA)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
P-CaCl2 and D_PBI for a grassland soil. In this case the P capacity is
left constant (so, A_P_AL is not changing) whereas the bio-available P
pool is increasing from 0.5 to 10 mg P / kg.
Potassium supply
Like N and P, potassium (K) an important element for crop growth.
Potassium is almost exclusively present in the soil in mineral form. The
amount of K in the soil can be divided into 4 fractions: * K^+- ions in
the soil solution; completely and directly available to the plant, but
insufficient to cover the needs of the crop * K-exchangeable; K adsorbed
to the clay and humus particles (adsorption complex; CEC). The exchange
between K in the soil solution and K adsorbed occurs rapidly: within
minutes to 24 hours * K-fixed or bound (in clay soils); the K enclosed
in the clay plates. Exchange between K-fixed and K-soil solution takes
days to months * K-mineral or K rock; becomes available through
weathering. The amount of K that becomes available through weathering
during a growing season is too small to be of agricultural interest.
The K supply is strongly controlled by the distribution of K over the
possible K pools in soil, being controlled by adsorption and desorption
processes, the cation exchange capacity of the soil and competing ions
in soil solution and present at the exchange complex. Building on
agronomic research from the last decade, the K supply is quantified for
grasslands using the plant available K fraction (measured via
CaCl2-extraction, K-CaCl2) as well as the CEC. For maize it is
quantified using K-CaCl2 and for arable fields its quantified from
K-CaCl2 and the CEC while accounting for the clay content, the organic
matter content and the pH of the soil.
To estimate the K supplying capacity of the soil, one can make use of
the function calc_potassium_availability. The function
requires the following input: the BRP crop code, the soil type, the
organic matter content, the clay content, the pH, the cation exchange
capacity (CEC), the occupation of the CEC with potassium (%) and the
directly available concentration of K as determined with a soil
extraction with 0.01M CaCl2.
For more details, see ?calc_potassium_availability.
# estimate potassium availability index (unitless)
dt[, D_K := calc_potassium_availability(B_LU_BRP, B_SOILTYPE_AGR, A_SOM_LOI, A_CLAY_MI,
A_PH_CC, A_CEC_CO, A_K_CO_PO, A_K_CC)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
K-CaCl2 and D_K for a grassland soil. In this case the occupation of the
CEC with K is left constant (so, A_K_CO_PO is not changing) whereas the
bio-available K pool is increasing from 5 to 500 mg K / kg.
Sulfur supply
Sulfur (S) is needed - along with nitrogen - for the formation of
proteins in the plant. Whether S supply from the soil is sufficient for
optimal production and quality depends on the crop’s S requirements and
the S supply in the soil. The S supply is determined by soil processes
and external sulfur supplies to the soil.
The amount of sulfur in the soil that is available for crop uptake is
determined by the mineral sulfur supply remaining in the soil after
winter (Smin), mineralization of sulfur in the soil during the growing
season (sulfur supply capacity), sulfur deposition, sulfur supply by
irrigation during cultivation, capillary rise of sulfur-containing
groundwater, and by possible losses. Sulfur supply, capillary rise, and
Smin are quantitatively the most important inputs of sulfur. However,
all three can vary considerably. The contribution from sulfur deposition
is only minor throughout the Netherlands. A substantial amount of sulfur
can also be supplied through irrigation with sulfurous spring water.
This supply, however, varies greatly, depending on the amount sprayed
and the sulfur content of the water.
To estimate the S supplying capacity of the soil, one can make use of
the function calc_slv. The function requires the following
input: the BRP crop code, the soil type, the agricultural region within
the Netherlands (used to estimate default S deposition rates), the
organic matter content, the total S content of the soil, and the bulk
density.
For more details, see ?calc_slv.
# estimate S supplying capacity
dt[, D_SLV := calc_slv(B_LU_BRP, B_SOILTYPE_AGR, B_AER_CBS,A_SOM_LOI,A_S_RT, D_BDS)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
total S and D_SLV for a grassland soil. In this case all soil properties
driving S supplying capacity are left constant whereas the total S pool
is increasing from 500 to 5000 mg S / kg.
Magnesium supply
Magnesium is an important element for crop growth, livestock health,
and livestock productivity. Deficiencies for magnesium often occur on
sandy soils with low organic matter and low pH. The supply of Mg for
arable fields as well as grassland fields on sandy soils is directly
related to the plant available Mg-content (Mg-CaCl2). For grassland
fields on clay and peat soils the Mg-supply is indirectly quantified
given the required composition of the grass (for intake by cows) and
depends on the CEC, the organic matter and clay content, pH, as well as
the K-availability assessed by K-CaCl2 and K-CEC.
To estimate the Mg supplying capacity of the soil, one can make use
of the function calc_magnesium_availability. The function
requires the following input: the BRP crop code, the soil type, the
organic matter content, the clay content, the pH, the cation exchange
capacity (CEC), the occupation of the CEC with potassium (%) and the
directly available concentration of both Mg and K as determined with a
soil extraction with 0.01M CaCl2.
For more details, see ?calc_magnesium_availability.
# estimate magnesium availability index (unitless)
dt[, D_MG := calc_magnesium_availability(B_LU_BRP, B_SOILTYPE_AGR, A_SOM_LOI,
A_CLAY_MI, A_PH_CC, A_CEC_CO,
A_K_CO_PO, A_MG_CC, A_K_CC)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
Mg-CaCl2 and D_MG for a grassland soil. In this case all soil properties
driving Mg availability in soil are left constant whereas the
bio-available Mg pool is increasing from 5 to 500 mg Mg / kg.
Copper supply
Copper (Cu) occurs in soil solution largely in a complexed form,
mainly with dissolved organic matter. Root uptake of Cu probably occurs
as free Cu ions (Cu2+). The availability of complexed Cu for uptake is
lower than that of Cu2+ and depends on the stability of the complex.
Complexation of Cu, however, may increase the mobility of Cu in soils.
Besides complexation of Cu to dissolved or solid organic matter, Cu can
be adsorbed to Fe-, Al-, and Mn-(hydr)oxideclay minerals. Cu desorbed
from the mentioned soil components is available for uptake. The degree
of adsorption increases at higher pH, which decreases the availability.
Other factors that influence Cu availability are nitrogen and phosphate
content. Nitrogen and Cu show positive interactions. Decreasing N use
will lead to lower levels in crops. Phosphate can drive Cu away from the
adsorption sites and this leads to Cu deficiency in the long run.
The supply and availability of Cu depends on the plant available
Cu-pool in soil (Cu-CaCl2) or the reactive Cu pool (Cu-HNO3) for both
arable and grassland soils. The optimum value is derived from historical
field experiments and is established on a level of 5 to 10 mg / kg. The
risk of Cu deficiency can be calculated based on the Cu content in the
soil and relevant soil characteristics that influence its availability.
The following measurements are used to calculate Cu plant availability:
land use, Cu-CaCl2, clay content, the organic matter content, and the
plant extractable levels of K and Mn. The last soil properties are used
for an empirical function to estimate Cu-HNO3 (the basis for fertilizer
recommendations based on long-term field experiments) from Cu-CaCl2
(being currently measured in agricultural laboratories). In OBIC, one
can make use of the function calc_copper_availability. The
function requires the input mentioned above.
For more details, see ?calc_copper_availability.
# estimate Cu availability index
dt[, D_CU := calc_copper_availability(B_LU_BRP, A_SOM_LOI, A_CLAY_MI, A_K_CC, A_MN_CC, A_CU_CC)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
Cu-CaCl2 and D_CU for a grassland soil. In this case all soil properties
driving Cu availability in soil are left constant whereas the
bio-available Cu pool is increasing from 5 to 500 ug Cu / kg.
Zinc supply
The processes involved in the behavior of zinc (Zn) in soil are the
same as for Cu. Besides Zn2+, Zn occurs in the soil solution in complex
form with dissolved organic matter. Binding of Zn to solid soil
constituents occurs to clay minerals, metal (hydr)oxides, and solid
organic matter. The affinity of Zn for binding to these materials is
lower than that of Cu. Zinc is taken up by plant roots as Zn2+. Because
the concentration of Zn2+ in the soil solution is low and Zn is not very
mobile, it is only transported over short distances. Therefore, a
sufficiently large root system is very important for a good Zn uptake.
The development of the root system is strongly influenced by the
phosphate supply of the crop. In herbaceous crops, the secretion of
phytosiderophores in response to a Fe or Zn deficiency strongly
increases Zn uptake. These organic compounds complex Zn and increase Zn
mobility in the soil, which facilitates Zn transport to the root and
uptake as Zn2+. A high pH, cold and wet conditions and a lot of organic
matter in the soil decrease the availability of Zn.
The supply of zinc depends on the plant availability of Zn such as
determined via CaCl2 extraction method (Zn-CaCl2), while accounting for
soil type, land use and pH. Critical threshold values for Zn has been
derived from optimum Zn contents of the growing crop. In OBIC, one can
make use of the function calc_zinc_availability. The
function requires the following input: land use, soil type, pH, and the
bioavailable Zn-content as measured via n extraction with 0.01M
CaCl2.
For more details, see ?calc_zinc_availability.
# estimate Zn availability index
dt[, D_ZN := calc_zinc_availability(B_LU_BRP, B_SOILTYPE_AGR, A_PH_CC, A_ZN_CC)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
Zn-CaCl2 and D_ZN for a grassland soil. In this case all soil properties
driving Zn availability in soil are left constant whereas the
bio-available Zn pool is increasing from 50 to 5000 ug Zn / kg.
Soil Acidity
The pH is a measure of the acidity of the soil. The pH influences the
soil quality and crop growth, among others through availability of
nutrients and (heavy) metals and activity of soil life. In addition, the
pH also influences various soil functions such as nutrient buffering and
aggregate stability. The optimum soil pH for crop growth differs per
crop. Potatoes prefer a lower pH and cereals, maize, sugar beet, and
field vegetables a higher pH. Organic matter reduces the negative effect
of pH on crop growth. On sandy soils with an organic matter content of
15%, the desired pH can be up to half a unit lower than on low organic
matter content soils. On clay soils the desired pH is higher than on
sandy soils. With a clay percentage above 10, the desired pH is half a
unit higher than with low clay percentages.
The optimum pH is determined in historical field experiments given
crop rotation plan, soil texture, soil organic matter, and initial pH.
The derivation of the optimum pH can be estimated via the OBIC using the
function calc_ph_delta. This function estimates how much
the pH has to increase by liming to be optimum for crop development. The
original empirical relationships are based on pH measurements done in
KCl-extraction. Since the current pH analysis methods all make use of
0.01M CaCl2, this pH value can easily be transformed to pH-KCl given an
empirical relationship between both.
For more details, see ?calc_ph_delta.
# estimate distance to required pH
dt[, D_PH_DELTA := calc_ph_delta(B_LU_BRP, B_SOILTYPE_AGR, A_SOM_LOI, A_CLAY_MI, A_PH_CC, D_CP_STARCH,
D_CP_POTATO, D_CP_SUGARBEET, D_CP_GRASS, D_CP_MAIS, D_CP_OTHER)]
An example of this function is illustrated below for both an arable
and a grassland field (left figure) as well for the relationship between
the initial and desired pH change for a grassland soil. In this case all
soil properties driving pH in soil are left constant whereas the initial
pH is increasing from 3 to 10.
Soil Cation Buffering
For good crop growth, sufficient nutrients must be available. Besides
the actual nutrient availability in soil solution, the capacity of a
soil to buffer nutrients is important to identify potential bottlenecks
for crop production. fertilization is needed when the buffering capacity
or speed of replenishment is insufficient. Soils can vary greatly in
their buffer capacity. Cations are adsorbed to negatively charged soil
particles (clay, organic matter, and oxides) and these cations may
become available through exchange. For example, a growing plant extracts
K+ from the soil solution. The adsorption complex will start to resupply
because the amount of K+ in the soil solution has decreased. Once again,
a balance is established between the K+ concentration in the soil
solution and the quantity of K+ adsorbed. In practice, soils with a
higher CEC are usually more fertilized and there is a lower risk of
cation deficiencies during the growing season. In general, the optimum
CEC value is around 100 mmol+/kg. CEC levels below 30-40 mmol+/kg are
characterized by substantial crop limitation whereas values above 100
have no positive impact any more. The scientific underpinning of these
guidelines is still poor. In OBIC the soil fertility is positively
assessed in relation to the CEC and can be evaluated with the OBIC
function calc_cec.
For more details, see ?calc_cec.
# estimate importance of CEC supporting crop development
dt[, D_CEC := calc_cec(A_CEC_CO)]
Calculate series of physical soil functions
The open soil index quantifies and evaluates a series of physical
soil functions related to the supply of water and the rootability of the
top and subsoil. The different soil physical functions are illustrated
and explained below. Soil physical functions include the capacity of
soils to retain and supply water, to resist wind erosion, topsoil
sealing, subsoil compaction, and to deliver bearing capacity for
mechanic activities
Water Stress due to drought or wetness
The supply of water is of uttermost importance for crop development.
The water supply depends on weather conditions and the capacity of soils
to buffer and supply water during the growing season. Using long-term
field experiments for multiple crops, empirical relationships between
soil texture, ground water levels, and yield depressions due to drought
or too wet conditions have been developed (Van Bakel, 2005; Huinink,
2018). Within OBIC the crop yield response to drought stress or
wetnessstress can be estimated via the function
calc_waterstressindex, requiring as input a soil code
(representing unique combinations of soil type and geohydrological
conditions controlling water availability), crop type, and groundwater
level.
For more details, see ?calc_waterstressindex.
# reformat GWL_CLASS
dt[, B_GWL_CLASS := format_gwt(B_GWL_CLASS)]
# estimate risk on yield reduction to drought stress or wetness stress
dt[, D_WSI_DS := calc_waterstressindex(B_HELP_WENR, B_LU_BRP, B_GWL_CLASS, WSI = 'droughtstress')]
dt[, D_WSI_WS := calc_waterstressindex(B_HELP_WENR, B_LU_BRP, B_GWL_CLASS, WSI = 'wetnessstress')]
An example of this function is illustrated below for both an sandy
and a clay soil given variation in the groundwater levels. In the left
figure the yield reduction to drought stress (D_WSI_DS, red) and wetness
stress (D_WSI_WS, green) are estimated for five fields with different
soil types and crops. In the right figure the impact of variable
groundwater dynamics are estimated for a single field.
Sealing Soil Surface and Wind Erodibility
Sealing is the process whereby soil aggregates disintegrate under the
influence of rain. The impact of raindrops causes a shifting of soil
particles (Locher and De Bakker 1990). In
the process, clay and silt particles clog the pores between the sand
particles or the soil aggregates. This creates a slurry layer that forms
a crust after drying. This hinders the gas exchange and increases the
resistance of germinating seed.
Wind erosion can occur in a dry spring or autumn when the soil is
(partly) bare. Wind erosion causes a decrease in organic matter content,
moisture retention capacity, chemical soil fertility, and biological
activity in a soil. Furthermore, wind erosion can spread diseases and
weeds, expose germinating seeds, and damage young plants by
sandblasting.
The vulnerability of soils to sealing and wind erosion is derived
from those properties controlling the susceptibility for both risks.
These include the clay content as well as the organic matter content,
where the vulnerability for sealing is derived from field expert-based
observations and associated yield depression (J.
Th. M. Huinink 2018; Heeres and Erp 1999) in particular for some
arable crops. The presence of soil sealing can be estimated via the
function calc_sealing_risk whereas the risk for soil
erosion due to wind is estimated via the function
calc_winderodibility. The wind erodibility can be estimated
from the inputs land use, clay and silt content of the topsoil whereas
the risk for sealing depends on the clay content as well as the organic
matter content of the soil.
Wind erosion is highly controlled by the mineralogical composition
and texture as well as the presence of growing crops. Using laboratory
experiments from wind tunnels, a exponential function has been developed
to estimate the erodibility risk for soils, given the clay and silt
content of a field. Grasslands are not susceptible for these two
risks.
For more details, see ?calc_sealing_risk and
?calc_winderodibility.
# estimate the presence / risk for surface sealing and wind erodibility
dt[, D_SE := calc_sealing_risk(A_SOM_LOI, A_CLAY_MI)]
dt[, D_WE := calc_winderodibility(B_LU_BRP, A_CLAY_MI, A_SILT_MI)]
An example of these functions is illustrated below for an arable soil
with variable clay content for both an cropland (with organic matter
levels of 3.5%) and a grassland soil (with organic matter levels of 5%).
Soil sealing is a potential risk and this risk is evaluated in the
indicator function (explained and illustrated later) given the land use
present. The wind erodibility is declining with the clay content and is
not relevant for grassland due to the permanent crop cover.
Aggregate Stability and Crumbleability
Crumbleability is an indication of the ease with which the soil can
be broken up or crumbled and of the moisture range within which this is
possible. The crumbleability of a soil is determined by the binding
between soil aggregates. The lower the degree of crumbling, the more
energy is required and the heavier tractors and equipment are needed for
working the soil. This requires (additional) investments and higher fuel
consumption, while the end result - even after additional tillage - is
poorer.
Similarly to the vulnerability to sealing and wind erodibility, the
crumbleability of a soil (a measure for aggregate stability) as well as
the potential risk for yield depressions (crop specific) can be derived
from the clay content, the organic matter content, and the pH (J. Th. M. Huinink 2011). Aggregate stability is
additionally evaluated given the cation occupation of the cation
exchange capacity. Clayey soils with 80% Ca, 8% Mg, and about 3.5% K are
recognized as soils with more stable aggregates due to the influence of
electrostatic bindings of divalent cations. Within OBIC these two soil
functions are calculated using calc_crumbleability and
calc_aggregatestability.
For more details, see ?calc_crumbleability and
?calc_aggregatestability.
# assess the crumbleability and aggregate stability
dt[, D_CR := calc_crumbleability(A_SOM_LOI, A_CLAY_MI,A_PH_CC)]
dt[, D_AS := calc_aggregatestability(B_SOILTYPE_AGR,A_SOM_LOI,A_K_CO_PO,A_CA_CO_PO,A_MG_CO_PO)]
To illustrate how both functions are estimated in OBIC, we firstly
show the dependency of the crumbleability to varying clay content using
a constant soil organic matter level of 3.5%. As shown below, the
crumbleability starts at a high value of 10 and gradually declines down
to a value of 6 for soils with a clay content of about 25%. The
aggregate stability depends mainly on the calcium occupation of the CEC.
In the figure below the distance to the optimum CEC occupation is
visualized for a series of soils varying in Ca, Mg and K occupation for
a soil where 100% of the CEC is occupied with a variable contribution of
the three cations. The highest aggregate stability is found when the
distance to the optimum is the lowest, being around a Ca occupation of
about 85% of the CEC.
Subsoil compaction
Soil compaction is caused by the use of excessively heavy machinery
or by driving over and/or tilling soil with insufficient bearing
capacity. Compaction can lead to poor rooting of the soil, limiting the
absorption of water and nutrients. On heavy soils, compaction mainly
occurs in the soil surface, while on lighter soils there is a risk of
subsoil compaction, such as plough-soil formation. Compaction decreases
the workability of soils and can reduce the water retention capacity of
the soil and impede water transport to deeper layers. This can lead to
an increased risk of surface run-off of nutrients and soil particles.
Soil compaction in the soil can be eliminated by ploughing. Subsoil
compaction is almost impossible to eliminate.
The risk of subsoil compaction for each field was assessed using soil
texture, land use and a soil compaction model SOCOMO. The model
determines whether the usual wheel loads for that land use exceed the
strength of the subsurface in wet or humid conditions. Subsequently it
was determined on the basis of the soil properties and groundwater
levels whether the subsurface is extra sensitive to compaction or
whether natural recovery is possible due to, for example, drought
shrinkage. Strength, land use, and soil properties together determine
the risk of subsoil compaction. The presence of subsoil compaction is
derived from a national map with the estimated risk. As such, there is
no calculation used. Recent field experimental data support the accuracy
of this risk assessment map.
Visual Soil Assessment
Within the OBIC, the estimates of aggregate stability and risk of
subsoil compaction can be adapted to local site specific insights
derived from the Visual Soil Assessment Methodology (Sonneveld, Heuvelink, and Moolenaar 2014).
Visual soil assessments (VSA) is an assessment of soil quality in the
field, by digging a hole and assessing several soil quality indicators
visually. Soil quality indicators are: grass cover, number of roots,
number of biopores, soil color, soil structure, soil compaction, and
number of gray spots. Visual soil assessments are more and more used by
farmers in the Netherlands, but not specifically developed for various
soil types.
Below is illustrated how the obic_field wrapper deals with the
parameters derived from the VSA methodology. The score derived from the
original risk assessment map for subsoil compaction is overwritten with
the relevant VSA indicators when When scores are present for the
presence of earthworms (A_EW_BCS), the occurrence of subsurface
compaction (A_SC_BCS), limited root development (A_RD_BCS), ponding in
the spring (wet conditions after rainfall, A_P_BCS) and clear presence
of visible tracks / rutting or trampling on the land (A_RT_BCS).
Similarly, the soil aggregate stability is adapted when VSA indicators
are available for earthworm density (A_EW_BCS), soil structure
(A_SS_BCS), and presence of cracks in the topsoil (A_C_BCS).
# overwrite soil physical functions for compaction when BCS is available
dt[,D_P_CO := (3 * A_EW_BCS + 3 * A_SC_BCS + 3 * A_RD_BCS - 2 * A_P_BCS - A_RT_BCS)/18]
dt[,D_P_CO := pmax(0, D_P_CO)]
dt[,I_P_CO := fifelse(is.na(D_P_CO),I_P_CO,D_P_CO)]
# overwrite soil physical functions for aggregate stability when BCS is available
dt[,D_P_CEC := (3 * A_EW_BCS + 3 * A_SS_BCS - A_C_BCS)/12]
dt[,D_P_CEC := pmax(0, D_P_CEC)]
dt[,I_P_CEC := fifelse(is.na(D_P_CEC),I_P_CEC,D_P_CEC)]
In the left figure below one can see how the soil compaction risk is
adapted when information is known from the Visual Soil Assessment. The
soil was originally evaluated as a soil with low compaction, resulting
in a high soil compaction score (the distance to target is small). When
all observations of the VSA have a high quality score (the value 2) then
the score remains the same. As soon as the observations of the VSA show
bottlenecks in the soil structure or rootability (the field score
becomes zero) then the soil compaction score is declined to almost zero
(the distance to target is huge). Similarly, the aggregate stability
score can be adapted, as shown here for a soil with a moderate aggregate
stability index. When field observations support a conclusion for the
soil that the aggregate stability is good (score = 2) then the aggregate
stability index is corrected to the maximum index a soil can retrieve
(the value 1). In contrast, when field observations support the
conclusion of serious bottlenecks for aggregate stability, then the
index declines to almost zero.
Water retention in topsoil
The moisture characteristic of a soil depends on its physical
properties, texture, and structure. The texture of a soil is determined
by its clay, loam, and sand content. In addition, almost all soils
contain organic matter. The fine soil particles, together with the
organic matter, contribute to aggregate formation (and thus to the soil
structure). The size, shape, and arrangement of the soil particles and
aggregates, and pores, determine the soil’s capacity to retain water.
Large pores are able to conduct more water faster than small pores,
moreover, removing water from large pores will require less energy than
removing water from small pores. When a soil is at field capacity, the
moisture state is such that all the water in the macro pores has been
replaced by air under the influence of the gravitational potential. The
water that is still present in the soil is retained in micro pores. The
prevailing potential at field capacity can vary from soil to soil but
usually varies between -0.1 bar (sandy soil) to -0.3 bar (loamy soil).
When water is retained to such an extent that it is no longer available
for crop uptake, this is known as the wilting point. The water is mainly
present as a film around individual soil particles. The potential under
these conditions is around -18 bar. The amount of moisture present
between field capacity and wilting point is defined as the amount of
plant-available water.
The review study of various soil health instruments (E. K. Bünemann et al. 2016) identifies a
variety of indicators that can be used to gain more insight into the
water retaining capacity of a soil. Frequently used indicators are the
amount of plant-available water (14 x), the water holding capacity (11
x), the moisture content at field capacity (11 x), and the saturated
permeability (10 x). These indicators can be measured or estimated
indirectly via so-called pedotransfer functions (Wösten et al. 2001).
The OBIC includes functions to derive the following water-related
indicators in function calc_waterretention:
- the moisture content at wilting point and field capacity
- The amount of plant available water (mm)
- the flow limit or porosity, also called water holding capacity,
and
- the saturated permeability.
The basic indicator used in the OBIC is the amount of plant available
water. The capacity of the soil to buffer water during the growing
season is estimated from pedotransferfunctions (pdf) for plant available
water in the topsoil. The default pdf is derived from a European
database, and enables one to estimate the van Genuchten parameters for
the pF-curve. Other options are also possible.
For more details, see ?calc_waterretention.
# estimate the plant available water in topsoil
dt[, D_WRI := calc_waterretention(A_CLAY_MI,A_SAND_MI,A_SILT_MI,A_SOM_LOI,type = 'plant available water')]
# estimate the water holding capacity in topsoil
dt[, D_WRI := calc_waterretention(A_CLAY_MI,A_SAND_MI,A_SILT_MI,A_SOM_LOI,type = 'water holding capacity')]
# estimate the moisture content of the wilting point in topsoil
dt[, D_WRI := calc_waterretention(A_CLAY_MI,A_SAND_MI,A_SILT_MI,A_SOM_LOI,type = 'wilting point')]
# estimate the moisture content of the field capacity in topsoil
dt[, D_WRI := calc_waterretention(A_CLAY_MI,A_SAND_MI,A_SILT_MI,A_SOM_LOI,type = 'field capacity')]
# estimate the saturated permeability in topsoil
dt[, D_WRI := calc_waterretention(A_CLAY_MI,A_SAND_MI,A_SILT_MI,A_SOM_LOI,type = 'Ksat')]
Below we illustrate how the amount of plant available water (in mm)
changes with clay content, sand content, silt content and soil organic
matter content. All other soil properties are assumed to be
constant.
Calculate series of biological soil functions
The open soil index quantifies and evaluates a series of soil
biological functions related to the composition of the microbiome,
suppression of soil borne pests and plagues, and plant parasitic
nematodes.
Potentially mineralizable nitrogen
The activity of soil fungi and bacteria has been measured via
incubation trials for decades. In such incubation trials, the
decomposition of soil organic nitrogen is measured over a period of
time. The amount of nitrogen that mineralizes in such trials is called
the ‘potential mineralizable nitrogen’(PMN). This indicates the ability
of the soil to provide a crop with readily available nitrogen. In the
Netherlands, this parameter is also used as an indicator for activity of
soil microbes. This is possible because during the incubation, a soil
sample is submerged in water, creating an anaerobic environment, killing
aerobic bacteria and fungi, which, together with some labile organic
matter, are decomposed by anaerobic soil microbes.
For more information see ?calc_pmn.
# calculate the index for the potential mineralizable nitrogen pool
dt[, D_PMN := calc_pmn(B_LU_BRP, B_SOILTYPE_AGR, A_N_PMN)]
The PMN measured by routine laboratories in the Netherlands may be
overestimated. Therefore, a land-use dependent correction factor is
used. The PMN index is capped at 500. Below an example of this function
is given.
Disease resistance
The activity of the soil life is an indication of the general disease
resistance of the soil. When a soil food web is in balance, the soil’s
resistance to disease and pests is also optimal. The soil’s resistance
to diseases and pests is often cited as a characteristic of a soil with
good biological soil quality. The idea behind this is that a soil with a
well-developed soil food web will be in balance, which means that strong
multiplication of parasitic soil organisms is inhibited by other soil
life. Mechanisms include competition for food or infection sites on the
root, eating the pathogens before they have had a chance to multiply
(myco-parasitism), or secreting (specific) substances that pathogens
cannot tolerate (antibiosis or soil fungistasis).
Organic matter serves as a food source for soil life and influences
the living environment of soil life through its effects on soil
structure and water holding capacity. The quantity and quality of
organic matter can therefore be used as an indicator for the quantity
and activity of soil life, and thus as an indicator for general soil
resilience.
At low organic matter concentrations, the contribution of organic
matter to soil life is negligible. A soil organic matter concentration
between 4% and 10% likely creates the best environment for good disease
resistance.
For more information see ?ind_resistance.
# Calculate disease resistance
dt[, I_B_DI := ind_resistance(A_SOM_LOI)]
Earthworm density
Earthworms are some of the largest fauna found in agricultural soils
and through their tunneling affect nutrient cycling and soil structure.
Analysis and interpretation of earthworm diversity is not regularly done
on Dutch agricultural soils. Earth worm density, the number of
individual worms in a volume of soil, is one of the things studied in
the Visual Soil Assessment (see Visual Soil Assessment for more
information).
Evaluate Soil Management
Unlike other soil functions, soil management is hard to evaluate
quantitatively. We introduced the expert-judgement driven framework of
the Sustainable Soil Management label (Van der Wal, 2016). This label
was designed in 2016 by a group of soil scientists and consultancy
workers in the Netherlands to implement sustainable soil management
within certification protocols of relevant chain parties in the
agricultural sector. A team of soil experts from research and practice
made a selection of measurable and verifiable soil management measures
that positively contribute to the ecosystem functions of the soil, and
qualitatively assessed their impact on the soil quality while accounting
for two land use categories and three soil type categories. Using this
expert driven management label, the soil management can be
systematically and quantitatively evaluated on field scale. Besides the
current management practices, explicit attention is given to measures
supporting soil organic matter build-up in soils, supporting the key
role of soil organic matter for soil fertility and other ecosystem
services. Because changes in soil organic matter are difficult to
measure, an estimate is made of the net supply or removal of Effective
Organic Matter based on the crop rotation plan and the current manure
practices according the regulations present. This balance is indicative
of the expected developments in the organic matter content of the
soil.
Measures
The measures taken on a parcel are evaluated according to a grading
system. For arable, maize, and grassland, different measures are
applicable reflecting the sustainability of soil management. For arable,
measures include; 80% of year green cover, >40% rest crop in
rotation, >40% deep rooting dormant crop in rotation, <25% potato
in rotation, use of early cultivars, net positive organic matter
balance. Specifically for maize, measures include: undersowing of grass,
use of catchcrop after harvest (only on clay). For grass, points can be
gained for the grassland age, use of drag hose fertilization, use of
grass/clover mixtures. For grass on peat points can also be received for
using underwaterdrainage and maintenance of ditches.
Crop rotation and SOM balance
A field can receive points for having a positive soil organic matter
balance. A function is included to estimate the organic matter input and
decomposition. For the calculation of the organic matter balance the
parcels’ crops, organic matter concentration and P status are required,
as well as the management aspects compost application frequency and
sowing of catch crops after main crop.
Below, examples are give of how to calculate the organic matter
balance and the management index. The management index requires inputs
that are not obligatory for the wrapper function
obic_field. The function add_management will
check the presence of management parameter values and give defaults
based on soiltype and crop when values are missing. Furthermore,
information on the crop rotation and on the age of grassland are
calculated by calc_rotation_fraction and
calc_grass_age respectively.
# Calculate organic matter balance
dt[, D_SOM_BAL := calc_sombalance(B_LU_BRP,A_SOM_LOI, A_P_AL, A_P_WA, M_COMPOST, M_GREEN)]
# add management when input is missing
cols <- c('M_GREEN', 'M_NONBARE', 'M_EARLYCROP','M_COMPOST','M_SLEEPHOSE','M_DRAIN','M_DITCH','M_UNDERSEED',
'M_LIME', 'M_NONINVTILL', 'M_SSPM', 'M_SOLIDMANURE','M_STRAWRESIDUE','M_MECHWEEDS','M_PESTICIDES_DST')
dt[, c(cols) := add_management(ID,B_LU_BRP, B_SOILTYPE_AGR,
M_GREEN, M_NONBARE, M_EARLYCROP,M_COMPOST,M_SLEEPHOSE,M_DRAIN,M_DITCH,M_UNDERSEED,
M_LIME, M_NONINVTILL, M_SSPM, M_SOLIDMANURE,M_STRAWRESIDUE,M_MECHWEEDS,M_PESTICIDES_DST)]
# calculate grass age
dt[, D_GA := calc_grass_age(ID, B_LU_BRP)]
# Calculate the crop rotation fraction
dt[, D_CP_STARCH := calc_rotation_fraction(ID, B_LU_BRP, crop = "starch")]
dt[, D_CP_POTATO := calc_rotation_fraction(ID, B_LU_BRP, crop = "potato")]
dt[, D_CP_SUGARBEET := calc_rotation_fraction(ID, B_LU_BRP, crop = "sugarbeet")]
dt[, D_CP_GRASS := calc_rotation_fraction(ID, B_LU_BRP, crop = "grass")]
dt[, D_CP_MAIS := calc_rotation_fraction(ID, B_LU_BRP, crop = "mais")]
dt[, D_CP_OTHER := calc_rotation_fraction(ID, B_LU_BRP, crop = "other")]
dt[, D_CP_RUST := calc_rotation_fraction(ID, B_LU_BRP, crop = "rustgewas")]
dt[, D_CP_RUSTDEEP := calc_rotation_fraction(ID, B_LU_BRP, crop = "rustgewasdiep")]
# Calculate series of management actions
dt[, D_MAN := calc_management(A_SOM_LOI,B_LU_BRP, B_SOILTYPE_AGR,B_GWL_CLASS,
D_SOM_BAL,D_CP_GRASS,D_CP_POTATO,D_CP_RUST,D_CP_RUSTDEEP,D_GA,
M_COMPOST,M_GREEN, M_NONBARE, M_EARLYCROP, M_SLEEPHOSE, M_DRAIN,
M_DITCH, M_UNDERSEED, M_LIME, M_NONINVTILL, M_SSPM,
M_SOLIDMANURE,M_STRAWRESIDUE,M_MECHWEEDS,M_PESTICIDES_DST
)]
Example of the soil organic matter balance and management on five
fields from the Binnenveld dataset.
Integrating Soil Functions into OBIC scores
The Open Soil Index is a number ranging between 0 to 1, that
holistically represents the soil quality as well as its management. The
score is field specific, accounting for the soil type, geohydrological
site properties and the crop rotation sequence of the last decade. The
final score can be decomposed to aggregated indicators for different
themes (chemical, physical, biological, and management), and these can
be further broken down in to indicators, representing an weighted
evaluation of soil functions over a period of time. The indicator (or
soil function score) for each soil function, ranges between 0 to 1 and
reflects the current situation given its deviation from a target
condition of that specific soil function. With this hierarchical
structure, the OBI offers both integral assessment (i.e. whether a soil
is overall good or not) and specific assessment (i.e. which soil
functions are poorly evaluated and to what extent these soil functions
need to be adapted to improve the overall soil quality to the “optimum
situation”).
Evaluating soil functions
Many of the soil function values calculated in the OBIC have a unit
and a target value. D_NLV for example is the nitrogen producing capacity
of the soil and should have a value between -30 and 250. However, values
calculated for individual soil functions have different units making it
complex to integrate into one holistic value. Nor is it easy to assess
whether a given value is good or whether it requires improvement.
Therefore, soil functions are evaluated to and transformed into an index
reflecting the distance to target. These indicators have a value between
0 and 1, 0 being very poor and 1 being excellent (optimal for
agricultural production). This way, the target value is clear and its
easy to see whether an indicator on a field warrants a lot of
improvement or not. Additionally, such scores can easily be turned into
scores ranging from 0-10 which is a commonly used scale for grading, and
therefore easy to interpret.
The OBIC package has functions that transform the value of a soil
function into a score. Examples of such functions are
ind_nitrogen(), ind_sealing(),
ind_pmn() and ind_nretention(). Some of these
functions only require the soil function’s value. Others may need soil
type or the cultivated crop as these parameters may require different
evaluation for specific soil types or crops rotation schemes.
# Be aware these functions below are not given here to be evaluated.
# They illustrate how the different indices can be evaluated (do not execute them here)
# Calculate indicators for soil chemical functions
dt[, I_C_N := ind_nitrogen(D_NLV, B_LU_BRP)]
dt[, I_C_P := ind_phosphate_availability(D_PBI)]
dt[, I_C_K := ind_potassium(D_K,B_LU_BRP,B_SOILTYPE_AGR,A_SOM_LOI)]
dt[, I_C_MG := ind_magnesium(D_MG, B_LU_BRP, B_SOILTYPE_AGR)]
dt[, I_C_S := ind_sulfur(D_SLV, B_LU_BRP, B_SOILTYPE_AGR, B_AER_CBS)]
dt[, I_C_PH := ind_ph(D_PH_DELTA)]
dt[, I_C_CEC := ind_cec(D_CEC)]
dt[, I_C_CU := ind_copper(D_CU,B_LU_BRP)]
dt[, I_C_ZN := ind_zinc(D_ZN)]
# Calculate indicators for soil physical functions
dt[, I_P_CR := ind_crumbleability(D_CR, B_LU_BRP)]
dt[, I_P_SE := ind_sealing(D_SE, B_LU_BRP)]
dt[, I_P_DS := ind_waterstressindex(D_WSI_DS)]
dt[, I_P_WS := ind_waterstressindex(D_WSI_WS)]
dt[, I_P_DU := ind_winderodibility(D_WE)]
dt[, I_P_CO := ind_compaction(B_SC_WENR)]
dt[, I_P_WRI := ind_waterretention(D_WRI)]
dt[, I_P_CEC := ind_aggregatestability(D_AS)]
dt[, I_P_WO := ind_workability(D_WO)]
# Calculate indicators for soil biological functions
dt[, I_B_DI := ind_resistance(A_SOM_LOI)]
dt[, I_B_SF := ind_pmn(D_PMN)]
# Calculate indicators for environment
dt[, I_E_NGW := ind_nretention(D_NGW, leaching_to = "gw")]
dt[, I_E_NSW := ind_nretention(D_NSW, leaching_to = "ow")]
Some of these indicator functions internally use an evaluation
function such as evaluate_logistic() and
evaluate_parabolic(). For more information on these
functions or logistic functions in general see
?evaluate_logistic(), ?evaluate_parabolic(),
or link
to Wikipedia. When logistic evaluation is used, there is no linear
relation between the an indicators value and its score. Often the
evaluation is set up so that lower values gain increasingly lower
scores. In other words, poor performance is evaluated more stringent
than good performance. Below, the relation between a soil function
values and their scores (index values) is given. An example of logistic
evaluation can be found in I_P_WS (water stress)
The indicator for management based on the point system of the label
sustainable soil management has a linear relation between the number of
points and the indicator score.
Crop and soil dependent applicability of functions
Not all indicators are relevant for all combinations of soil type and
crop. For example, I_P_DU (wind erodibility) is not
relevant on permanent grassland, as wind erosion is not a problem on
these parcels. The table weight.obic is used to determine
whether an indicator is relevant for a given parcel. Crops are
differentiated into the categories arable, grassland, maize, and nature
according to the crop_category from the table crops.obic.
In soil type a differentiation is made between peat and non peat soils.
If an indicator is not relevant for a given parcel, its score will not
be used in further aggregation.
# load weights.obic (set indicator to zero when not applicable)
w <- as.data.table(OBIC::weight.obic)
# Add years per field
dt[,year := .I, by = ID]
# Select all indicators used for scoring
cols <- colnames(dt)[grepl('I_C|I_B|I_P|I_E|I_M|year|crop_cat|SOILT',colnames(dt))]
# Melt dt and assign main categories for OBI
dt.melt <- melt(dt[,mget(cols)],
id.vars = c('B_SOILTYPE_AGR','crop_category','year'),
variable.name = 'indicator')
# add categories relevant for aggregating
# C = chemical, P = physics, B = biological, BCS = visual soil assessment
# indicators not used for integrating: IBCS and IM
dt.melt[,cat := tstrsplit(indicator,'_',keep = 2)]
dt.melt[grepl('_BCS$',indicator) & indicator != 'I_BCS', cat := 'IBCS']
dt.melt[grepl('^I_M_',indicator), cat := 'IM']
# Determine number of indicators per category
dt.melt.ncat <- dt.melt[year==1 & !cat %in% c('IBCS','IM')][,list(ncat = .N),by='cat']
# add weighing factor to indicator values
dt.melt <- merge(dt.melt,w[,list(crop_category,indicator,weight_nonpeat,weight_peat)],
by = c('crop_category','indicator'), all.x = TRUE)
# calculate correction factor for indicator values (low values have more impact than high values, a factor 5)
dt.melt[,cf := cf_ind_importance(value)]
# calculate weighted value for crop category
dt.melt[,value.w := value]
dt.melt[grepl('veen',B_SOILTYPE_AGR) & weight_peat < 0,value.w := -999]
dt.melt[!grepl('veen',B_SOILTYPE_AGR) & weight_nonpeat < 0,value.w := -999]
Holistic OBI score
The integration of different soil functions into one score and their
relevance in achieving a specific target (like crop yield) is often
ignored in soil quality assessments (i.e., each function contributes
equally), is based on expert-judgement or derived from multi-variate
statistics analyzing linkages among soil functions and soil and field
properties within large datasets. Large databases are needed in which
all relevant soil properties and functions have been determined as well
as (historical) management. Unfortunately, these databases are scarce so
that expert driven weighing procedures are introduced. Currently, the
total OBIC score is a weighted average of the major soil functions
(aggregated indicators per category) where the weight of each major soil
function is determined by the number of indicators underlying the major
soil function.
# merge out with number per category
out.score <- merge(out.score,dt.melt.ncat, by='cat')
# calculate weighing factor depending on number of indicators
out.score[,cf := log(ncat + 1)]
# calculated final obi score
out.score <- rbind(out.score[,list(cat,value)],
out.score[,list(cat = "T",value = sum(value * cf / sum(cf)))])
The holistic OBI score is given when the argument output in
obic_field() or obic_field_dt() is set to
‘all’, ‘scores’ or ‘obic_scores’
# For example
OBIC::obic_field_dt(binnenveld[ID == 1], output = 'scores')
OBIC::obic_field_dt(binnenveld[ID == 1], output = 'obic_score')
Will give:
#> Key: <ID>
#> ID S_B_OBI_A S_C_OBI_A S_E_OBI_A S_M_OBI_A S_P_OBI_A S_T_OBI_A
#> <int> <num> <num> <num> <num> <num> <num>
#> 1: 1 0.998 0.86 0.965 0.586 0.216 0.672
#> Key: <ID>
#> ID S_T_OBI_A
#> <int> <num>
#> 1: 1 0.672
