290 A. Miyata et al. Agricultural and Forest Meteorology 102 2000 287–303
used as a reference scalar instead of CO
2
. These tracer methods are advisable particularly when the
nighttime fluxes are being investigated because calm periods may invalidate the aerodynamic approach
Denmead, 1994. In this study, we choose CO
2
as a tracer because the nighttime vertical gradients of CO
2
mixing ratio can be measured more accurately than those of potential temperature or water vapor.
3. Experimental
3.1. Site description IREX96 was conducted at the Hachihama experi-
mental farm of Okayama University, Japan 34
◦
32
′
N, 133
◦
56
′
E, 2 m above sea level. The farm, approx- imately 300 m×300 m, is situated in a paddy area
within reclaimed land facing Kojima Bay in the south- ern part of Okayama Prefecture. The soil is mainly clay
60; Kobashi et al., 1968. Rice cultivation on the farm has continued in a similar way every year since
1960. In 1996 rice Oryza sativa L.; cultivar Akebono was seeded to the dry paddy on 13 May with density
of 60 kg ha
− 1
and a row spacing of 27 cm. Irrigation started on 19 June and the field was flooded continu-
ously until 12 July. This was followed by an intermit- tent drainage practice with 4 days of flooding and 3
days drainage which continued until harvest on 30 Oc- tober. This intermittent drainage is aimed at removing
salt from the paddy fields. Neither compost nor rice straw were applied to the paddy, but slow-release-type
mineral fertilizers N, P, K=77, 77, 77 kg ha
− 1
were applied at the time of seeding. The dry matter yield of
1996 was 5930 kg ha
− 1
, which was 25 greater than the average yield from 1989 to 1995 4740 kg ha
− 1
. The measurement of CO
2
and CH
4
fluxes over the canopy was conducted from 6 to 13 of August, about a
month before heading of the rice plants on 5 Septem- ber. The paddy was drained from the afternoon of 6
August to the morning of 9 August, and was flooded to a depth of 8–10 cm for the remaining observation
period. The plant height was about 0.72 m above the water surface, and the leaf area index LAI measured
with a canopy analyzer LAI-2000, LICOR Inc., Lin- coln, NE, USA was 3.08±0.28 the mean±standard
deviation with a spatial variability from 1.6 to 3.9. Yamamoto et al. 1995 showed LAIs of rice plants
measured with the canopy analyzer agreed well with those by destructive measurement standard error was
0.28. Micrometeorological sensors and air inlets were
mounted on the masts at the center of the experi- mental farm. The fetch in the prevailing SE direction
exceeded 300 m, and footprint analysis following Schuepp et al. 1990 indicated that 90 of the
measured flux at a height of 2.2 m was expected to come from within the nearest 300 m of upwind area
Harazono et al., 1998.
3.2. Eddy covariance measurements Friction velocity u
∗
, and the fluxes of sensible heat H, water vapor E, and CO
2
F
CO2
, over the rice canopy were measured by the eddy covariance method. The
eddy covariance method has been widely used for CO
2
flux measurements above plant canopies and a useful summary of the technique can be found in
Leuning and Judd 1996. A three-dimensional sonic anemometer Solent, Model 1012R, Gill Instruments
Ltd., Lymington, UK with path length of 15 cm was installed at a height of 2.2 m above the water to mea-
sure the fluctuations of three components of wind velocity. Fluctuations in virtual temperature were
obtained from the vertical axis signal of the sonic anemometer Kaimal and Gaynor, 1991; Hignett,
1992. To measure fluctuations in the CO
2
and wa- ter vapor concentrations, a fast response infrared gas
analyzer with a 20 cm span open-path E009, Ad- vanet Inc., Okayama, Japan was installed at the same
height as the sonic anemometer with a horizontal sep- aration of 17 cm. The sensitivity of the gas analyzer
to CO
2
was calibrated before and after the experi- ment using three levels of standard gases between
300 and 400 ppmv CO
2
in N
2
, Takachiho Chemical Industrial Co. Ltd., Tokyo, Japan. The sensitivity of
the analyzer to water vapor was factory-calibrated in a thermostatic chamber before the experiment. The
data from the sonic anemometer and the gas ana- lyzer were sampled at 10 Hz using a 16-bit digital
data recorder DR-M2a, TEAC Co., Ltd., Tokyo, Japan.
The fluxes u
∗
, H, E and F
CO2
were calculated on a 30 min basis from the covariances between the
vertical wind velocity and corresponding quantities. A correction for path length averaging of the sonic
A. Miyata et al. Agricultural and Forest Meteorology 102 2000 287–303 291
anemometer and the gas analyzer, and that for sepa- ration of both sensors were applied following Moore
1986 and Leuning and Moncrieff 1990. The in- fluence of these corrections on each flux varies with
atmospheric stability, but the average magnitudes of the corrections are as follows. The correction for path
length averaging increased u
∗
and H by 0.5 and 2.9, respectively, while corrections for path length averag-
ing plus sensor separation increased E and F
CO2
by 11.8 and 12.6, respectively. The influence of density
fluctuations arising from H and E Webb et al., 1980 increased E by 4.9 and reduced F
CO2
by 10.1. Because we calibrated the CO
2
sensor using CO
2
in nitrogen i.e. dry conditions, we were unable to de-
termine the cross-sensitivity of the CO
2
gas analyzer to water vapor Leuning and Moncrieff, 1990. Had
we applied the correction with the cross-sensitivity found for their E009 instrument βα=1×10
− 3
in Eq. 8 of Leuning and Moncrieff 1990, the magnitude
of F
CO2
would increase by 8.8 on average. 3.3. Measurement of gas concentration profiles
CH
4
concentrations in sampled air were mea- sured using a non-dispersive infrared CH
4
analyzer GA-360E, Horiba Co. Ltd., Kyoto, Japan equipped
with a specially designed pre-conditioner to minimize the interference of non-methane hydrocarbons and
water vapor Harazono et al., 1995. The time con- stant of the analyzer was 8.5 s. The CH
4
analyzer was calibrated twice a day, around 0900 and 1700 hours
using two reference cylinders with high grade air con- taining 1.7 ppmv CH
4
Takachiho; certified accuracy is ±2. CO
2
concentrations were measured using a non-dispersive infrared CO
2
analyzer LI-6251, LICOR, which was operated with a time constant
of 1 s. The CO
2
analyzer was calibrated at the same time as the CH
4
analyzer using two cylinders with 350 and 400 ppmv CO
2
in N
2
Takachiho. Air inlets for sample air were mounted at eight
heights, 0.12, 0.24, 0.36, 0.48, 0.60, 0.72, 1.10 and 2.40 m above the water, and another inlet for refer-
ence air was mounted at 2.50 m. The reference air was required because the gas analyzers were operated
in the differential mode which detected the differ- ences in infrared absorption between the sample air
and the reference air. The gas concentrations at 1.10 and 2.40 m were used for the gas flux calculation by
use of the gradient method, while the whole profiles were used to infer sources and sinks of the gases in
the canopy using an inverse Lagrangian analysis as described by Leuning et al. 2000. Teflon diaphragm
pumps MAA-P108-HB, Gas Manufacturing Corp., Benton harbor, MI., USA and nylon tubing 10 mm
ID were used for air sampling. Air sampled at each inlet was drawn through an ice-trap to reduce mois-
ture content, into a cylindrical PVC buffer 70 dm
3
in volume; time constant is about 15 min, then pumped
to a T-junction, one arm of which was connected to a tube placed in a 60 cm deep water bubbler to control
the pressure and the flow rate in the sampling line. The third arm of each T-junction was connected to
a solenoid valve to permit selection of each air line in turn for gas analysis. The solenoid valves were
controlled by a data logger and a personal computer. The air in the selected line passed through flow me-
ters, dried further to a dew point temperature of 2
◦
C using a Peltier-cooled condenser DH-209, Komatsu
Electronics Inc., Tokyo, Japan, and then analyzed. The solenoid valve was switched every 2 min, and the
sampling sequence was as follows: Line 1 2.4 m, 2, 3, 4, 5, 6, 7, 8 0.12 m, 7, 6, 5, 4, 3, 2, 1. . . .
The full sampling sequence was thus completed in 30 min. This ‘staircase’ sampling technique eliminates
linear trends in measurement of gas concentration differences.
Gas concentration data were sampled and recorded every 5 s using an AD converter Green Kit-88,
Electric Systems Development, Tokyo, Japan and a personal computer. The mean of the data sampled
between 30 and 110 s after line switching was used to estimate the concentration at each height. After
1730 hours of 11 August, however, the CH
4
concen- tration was averaged between 80 and 110 s after line
switching because the CH
4
analyzer was operated in the slow mode with a time constant of 26 s. The
influence of insufficient response of the CH
4
analyzer in the slow mode on the average was estimated to
be less than 3, and was neglected. The standard error of the fluctuation of the analyzer’s output dur-
ing the averaging period was 2.5 ppbv for the CH
4
analyzer in the fast mode, 1.0 ppbv in the slow mode and 0.2 ppmv for the CO
2
analyzer. These standard errors were used to estimate uncertainties in calcu-
lated gas fluxes. The mean vertical difference of the gas concentration was calculated from 30 min means
292 A. Miyata et al. Agricultural and Forest Meteorology 102 2000 287–303
the average of consecutive two cycles of the profile measurement at 1.10 and 2.40 m.
3.4. Chamber measurement of CH
4
flux CH
4
fluxes were also measured using a closed chamber for comparison with the flux-gradient
method. A bottom-less chamber, 0.36 m
2
in area, 1 m in height, made of acrylic resin, with an electric fan
for circulation was employed for the measurement. Details of the chamber and air sampling method are
described in Yagi and Minami 1993. The measure- ment was conducted on 13 August at two sites in the
measurement plot, approximately 20 m to the west western site and 30 m to the east of the masts east-
ern site. At each site, two chambers were placed 4 m apart to examine the spatial variation of the flux.
Air temperature inside the chamber T
c
and soil tem- perature below it were monitored using thermistor
thermometers. Air was sampled four times at 10 min intervals by pumping air into a Tedlar bag GL Sci-
ence, Tokyo, Japan. The chamber was placed 5 min before the first air sampling, and was removed imme-
diately after the last forth sampling. Volume mixing ratios of CH
4
in the bags were analyzed using a gas chromatograph with a flame-ionization detec-
tor GC-9A, Shimadzu, Kyoto, Japan located in an air-conditioned laboratory. The volume mixing ratio
was converted to density using T
c
and the partial pressure of dry air in the chamber p
a
. The CH
4
flux was deduced from the rate of change of CH
4
den- sity with time as determined using linear regression.
Leakage into the chamber caused by air sampling had an insignificant effect on the flux measurement be-
cause sampling removed ∼1 4 dm
3
of the chamber volume.
3.5. Supplementary measurements Incident and reflected solar radiation, net radiation
and photosynthetically active radiation were measured respectively with an Epply-type pyranometer MR-22,
Eko, Tokyo, Japan, a net radiometer Q6, Radiation Energy Balance Systems Inc., Seattle, WA, USA and
a quantum sensor ML-020P, Eko. Soil heat flux was measured by three heat flux plates MF-81, Eko, and
the influence of the difference of thermal conductiv- ity between the plate 0.21 W m
− 1
K
− 1
and the soil ca. 1.0 W m
− 1
K
− 1
was corrected following Philip 1961. Water and soil temperatures at 2 and 5 cm
depth were measured with T-type thermocouples. Changes in heat storage in floodwater was estimated
from the change of water temperature. Water depth was measured with a float-type water gauge. The ver-
tical profiles of air temperature and relative humidity were measured using ventilated Platinum resistance
temperature sensors and capacitive humidity sen-
sors HUMITTER® 50Y, Vaisala, Helsinki, Finland mounted at the same heights as the air inlets.
3.6. Floodwater depth and meteorological conditions Water depth started decreasing in the morning of 6
August by drainage, and standing water disappeared at 1400 hours Fig. 1a. Irrigation started at 0900 hours
of 9 August, and water depth reached 10 cm around midday. The water level was maintained until the
afternoon of 11 August, and afterwards gradually decreased with cessation of irrigation.
Clear days continued during the experiment, but meteorological conditions were a little different from
day to day Fig. 1. Wind direction not shown in the figure was constant, southeast, and windspeed showed
clear diurnal variation: 2–3 m s
− 1
in the daytime ex- cept on 12 and 13 August, and declined to less than
0.5 m s
− 1
at night Fig. 1b. On 12 and 13 August, windspeed was higher than on the other days as the re-
sult of an approaching typhoon. The daily maximum air temperature at 2.4 m was 30–32
◦
C, and the daily minimum was 23–26
◦
C Fig. 1c. Saturation deficit of air increased gradually in the morning, and reached
a maximum of 9–15 g kg
− 1
in the late afternoon. On 10–11 August, higher air temperature and larger sat-
uration deficit prevailed. As shown in Fig. 1d, most of the net radiation in the
daytime was partitioned into latent heat flux λE λ is latent heat of vaporization of water, whereas H was
less than 50 W m
− 2
except on windy 13 August when it exceeded 80 W m
− 2
. H changed sign from positive upward transport in the morning to negative in the af-
ternoon. The Bowen ratio HλE on drained days 7–8 August was 0.08 on average for 0900–1500 hours,
while on flooded days 10–12 August it ranged from −
0.03 to 0.04. Further details of the energy bal- ance during IREX96 are given by Harazono et al.
1998.
A. Miyata et al. Agricultural and Forest Meteorology 102 2000 287–303 293
Fig. 1. Floodwater depth, surface energy balance and selected meteorological conditions during IREX96. a Floodwater depth d
w
, b windspeed at a height of 2.2 m U measured with a sonic anemometer and friction velocity u
∗
, c air temperature T
a
and saturation deficit of the air at a height of 2.4 m in mixing ratio D
a
, d net radiation R
n
, sensible heat flux H and latent heat flux λE.
4. Results and discussion
