Simulation of C and N dynamics

in soil and plants

R.A. Poluektov & V.V.Terleev


Agrophysical Research Institute,
St.-Petersburg, Russia

Model structure
Input data
Soil
Texture, bulk density, hygroscopy, wilting point, field
capacity, saturation point, saturation hydraulic conductivity
Climate (daily weather
values)
Minimum and maximum air temperature, minimum air
humidity, precipitation, average wind speed, sunshine
duration
Management Irrigation and fertilization regimes
Initial conditions
Sowing date; water and nitrogen content in one meter soil
layer; soil organic matter and mass of microbial population
in 0-30 cm layer
State variables and output
State variables
Soil water moisture, soil temperature, and nitrogen
content according to layers: 0-10, 10-20,,90-100 cm;
Physiological time (0 at emergency, 1 at anthesys, 2
at full ripening)
Output (daily variables)
Primary assimilates; development stages; leaf area index;
dry mass of the leaves, stems, roots and ears;
evapotranspiration; water storage and nitrogen content in
one meter soil layer; infiltration of soil water; nitrogen
leaching; grain yield
Submodels
Processes
Radiation regime of crop, turbulent exchange between
air and plant, photosynthesis and respiration, plant
development stages, crop transpiration and soil
evaporation, soil water dynamics, nitrogen
transformation in soil and plant
Parameters
Parameters of: photosynthesis unit (3 items); plant
development (610 items according to phases);
distribution keys (64 items according to plant organs);
hydrological constants (4); N-transformation in soil (5);
N-uptake by root (2)
Shell structure of AGROTOOL
Place selection
Place selection
Field
selection
Field
selection
Culture selection
Choice of the year
management and
the date of
forecast
Choice of the year
management and
the date of
forecast
D

S
E
D

S
E
Estimation
and
forecast
Model features
- Initialization is done by means of management program (Model shell), which constitutes simulation system
AGROTOOL (together with model itself) and includes selection of: simulation place (geographic coordinates and concrete
field); culture (spring and winter wheat, spring burley, winter ray, potatoes, oats, perennial grasses); management
(irrigation and fertilization regimes); task type (analysis, forecast, weather generation); calculation year; and initial state
(sowing date, water and nitrogen content in one meter soil layer).

- Resolution in time and space (profile) is following: basic time step is 24 h (units of
photosynthesis, water and nitrogen dynamics use hourly internal time step) basic spatial step on vertical direction is 10 cm
(up to 100 cm).

- Peculiarities of the model are:
New method of calculation of plant transpiration and soil water evaporation based on modification Penman-Monteith
method;
Adaptive distribution key for calculation of root/shoot ratio using C:N interaction in plant canopy;
Automotive system for calculation of the parameters of pedotransfer functions.

Model identification consists of 5 steps:
1) Calibration of water dynamics unit,
2) Determination of parameters of development unit,
3) Determination of water stress function,
4) Calibration of nitrogen dynamics unit,
5) Determination of parameters of forecast function.
Parameters controlling temp of plant
development:
T
0
biological zero,
0
C;
c
1
, coefficient of extra plant heating,
0
C;

opt
boundary of comfort zone for soil water potential, cm;
S
0
water stress coefficient;
T
Ph


boundary of development change, degree-days.
Water stress function
) ( _
) 1 (
SS B Wstr W W A = A

( )

=
=
+
=
j
l
s p
j
l
l E l E
l PR
j SS
0
0
) ( ) (
) (
) (


Wstr B a a SS a SS a SS _ = + + +
0 1 2
2
3
3

Correction of dry matter accumulation
Argument of water stress function
Stress function
Calculation of root:shoot ratio




Shoot

Root
CO
2
NO
2
, NH
4
NH
4
PrimAss
(Two flows model)
C and N transformation in soil









Soil organic
matter
Microbal
biomass
NH
4
+
Mineralization
Immobilization
Nitrification
NO
3
-
Immobilization

N uptake by
roots
Losses
Ficsation
Clay
minerals
Mineral
fertilizers

Denitrification
Losses
N
2
+H
2
O NH
3
) ( ) 1 ( ) (
) ( ) (
k c k W
k c k W
rs s
rs r
u = A
u = A


, ) ( ) (
, ) ( ) (
root c r rd
shoot c s sd
N R k W k N
N S k W k N
A = A
A = A


( )
}

+ O = A
RT
T k
N av
dt t k V k N
) 1 (
, ) ( ) 1 ( ) ( e
( ) ) ( ) 1 ( k k V N
N av
AO + O = A
) ( ) ( k W S k
r root
A = AO
) ( ) ( ) ( k N k N k N
av rd sd
= +
Distribution of PrimAss:
N demand by shoot
and root
N uptake by roots:
N balance:
Calculation of c
rs

Determination of root:shoot ratio
1- N-dependence
of crop,
2 N-uptake by
roots
0
1
2
3
0 0,2 0,4 0,6 0,8 1
Part of assimilates allocated to roots
N
i
t
r
o
g
e
n

a
b
s
o
r
b
e
d

b
y

c
r
o
p
1
2
Dependence of root:shoot ratio on N-doze
1- flowering
phase,
2 full
ripening
phase
0
0,05
0,1
0,15
0,2
0,25
0,3
0,35
0 20 40 60 80 100
Nitrogen fertilization dose, kg ha
-1
R
o
o
t
:
s
h
o
o
t

r
a
t
i
o
1
2
Dynamics of root:shoot ratio by
various N-fertilization
1- variant without N,
2 N=45 kg ha
-1
,
3 N=90 kg ha-1
0,0
0,1
0,2
0,3
0,4
0,5
0,6
0,7
0,8
0,9
0 10 20 30 40 50 60 70 80 90
Days of vegetation starting from sowing
R
o
o
t
:
s
h
o
o
r

r
a
t
i
o

1
2
3
( )
,
1
a
b
MH SP
MH

u
+

+ =
where
volumetric soil moisture,
matrix potential,
MH maximum hygroscopy,
SP saturation point,
a, b empirical parameters.
u

Model of water retention curve

Variants of calculation of hydrological constants
, , , ,
Variants Input data Results of calculation
1 , MH, WP, SP LC, FC, UC
2 , WP, SP, soil texture MH, LC, FC, UC
3 , MH, SP soil texture LC, WP, FC, UC
4 , SP MH, LC, WP, FC, UC
1' ,
S
, MH, WP LC, FC, UC, SP
2' ,
S
, WP, soil texture MH, LC, FC, UC, SP
3' ,
S
, MH, soil texture LC, WP, FC, UC, SP
4' ,
S
MH, LC, WP, FC, UC, SP
- soil bulk density,
S
- solid phase density, MH maximum hygroscopy,
SP - saturation point, WP wilting point, FC field capacity,
LC lower capillary moisture, UC upper capillary moisture.
0
1
2
3
4
5
6
0,0 0,1 0,2 0,3 0,4 0,5 0,6

4
3
2
1
Volumetric soil moisture u -du /d(pF), cm
3
cm
-3

LC
UC

p
F
=
l
o
g
1
0
(
-

)
,

w
h
e
r
e

-

m
a
t
r
i
x

p
o
t
e
n
t
i
a
l

c
m

H
2
O
1 water retention curve,
2 specific water capacity,
3 dependence of UC on
UC
,
4 - dependence of LC on
LC

Calculation of water retention curve for the soil of
Men'kovo experimentation station using the following
experimental data:
,
S
, MH.

0
1
2
3
4
5
6
0,0 0,1 0,2 0,3 0,4 0,5 0,6
Volumetric soil moisture u -du /d(pF), cm
3
cm
-3


p
F
=
l
o
g
1
0
(
-

)
,

w
h
e
r
e

-

m
a
t
r
i
x

p
o
t
e
n
t
i
a
l

c
m

H
2
O
Comparison of calculated and experimental data
o experimental points,
-.- - interpolated curve,
curve calculated
using experimental data

Computer system for estimation soil hydraulic parameters
Estimation of Badlauchstadt pedotransfer functions
This program was used for estimation of the parameters
included in pedotransfer functions. The experimental data for
soil texture and saturated hydraulic conductivity were used for
this purpose. Two additional data, apart from available MH
and SP, were necessary for estimation of the pF-curve
parameters. Such hydraulic soil parameters as field capacity
(FC) and wilting point (WP) were chosen for this purpose.
The comparison of simulated pF-curves with experimental
data is presented in the following Figs.
Comparison between simulated water retention curves and
experimental data sets presented by Franko et al.
(site Badlauchstadt)



Fig. 1. 20-24 cm Fig. 2. 45-49 cm Fig. 3. 115-119 cm

Comparison of simulated and real winter ray grain yield
(Menkovo experimentation station)
Dependence of spring barley grain yield
on N-dose (Menkovo experimentation station)
10
20
30
40
0 20 40 60 80 100 120
N-fertilization dose kg ha-1
G
r
a
i
n

y
i
e
l
d

d
t

h
a
-
1
1
2
3
1 - 2000 .
2 -
3 - 2004 .
. 8.7

Nitrates leaching (Menkovo experimentation station)
0
30
60
90
120
150
0 20 40 60 80 100 120
N-fertilization dose, kg ha
-1
N
-
N
O
3

l
e
a
c
h
i
n
g
,

k
g

h
a
-
1

y
e
a
r
-
1

1
3
2

Yield and dry mass
0
20
40
60
80
100
120
0 20 40 60 80 100 120 140
Days since planting
D
r
y

m
a
s
s

o
f

p
l
a
n
t

o
r
g
a
n
s
,

d
t

h
a
-
1
1
2
3
4
Dynamics of dry mass of potatoes plant organs.
Badlauchstadt, 2001 yr.
1 - leaves,
2 - stems,
3 - leaves + stems,
4 - tubers,
A experimental data for leaves.
Yield and dry mass
0
10
20
30
40
50
60
70 90 110 130 150 170
Days on Julian calender
D
r
y

m
a
s
s

o
f

p
l
a
n
t

o
r
g
a
n
s
,

d
t

h
a
-
1
1
2
3
4
Dynamics of dry mass of spring barley plant organs.
Badlauchstadt, 2000 yr.
1 - leaves,
2 - stems,
3 - aboveground,
4 - ears,
A - experimental data for aboveground mass.
Yield and dry mass
0
20
40
60
80
100
120
140
160
100 150 200 250 300
Days since sowing
D
r
y

m
a
s
s

o
f

p
l
a
n
t

o
r
g
a
n
s

d
t

h
a
-
1
1
2
3
4
Dynamics of dry mass of winter wheat plant organs.
Badlauchstadt, 2001 yr.
1 - leaves,
2 - stems,
3 - aboveground,
4 - ears,
A - experimental data for aboveground,
o - experimental data for ears.
Water status
10
15
20
25
30
0 20 40 60 80 100 120 140
Days since planting
W
a
t
e
r

s
t
o
r
a
g
e

i
n

o
n
e

m
e
t
e
r

l
a
y
e
r
,

c
m
Soil water dynamics under potato crop,
Badlauchstadt, 2001 yr.
A measurement data
Water status
10
15
20
25
30
40 60 80 100 120 140 160 180
Days on Julian calender
W
a
t
e
r

s
t
o
r
a
g
e

i
n

o
n
e

m
e
t
e
r

l
a
y
e
r
,

c
m
Soil water dynamics under spring barley crop,
Badlauchstadt, 2000 yr.
A - measurement data
Results of statistical treatment for water content
Culture/year
Mean value, cm

Error, cm

MSE, cm

Spring
barley/2000
19.0 -0.208 1.04
Potatoes/2001 22.4 -1.16 0.95
The error was calculated according to formula:

= =
i i i w
WS WSsim
n
Ew
n
E exp
1 1

where WSsim
i
is simulated soil water storage corresponding to i-th measurement, n is
total number of measurements. Mean square error (MSE) is the square root from the
variance of the errors Ew
i
.
Results of statistical treatment for dry mass
Relative error was calculated on formula:

=
i
i i
Bsim
B Bsim
n
RE
exp 1
,
where Bsim
i
is simulated value of dry mass, Bexp
i
corresponding experimental value,
n total number of measurements. Mean square error (MSE) was calculated as square
root from variance of RE
i
.
Culture/year
Relative error

MSE

Spring barley/2000 0.065 0.24
Potatoes/2001 0.061 0.30
Winter wheat/2001/02 -0.21 0.44
Conclusion
Generally, there are externally few things in
the World, which we really anything know
about. In the most cases it only seems to us
that we know.

Kharuki Murakami
Hunting on sheep



Thank you