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Comparative measurements and seasonal variations in energy and carbon

exchange over forest and pasture in South West Amazonia

Article  in  Theoretical and Applied Climatology · June 2004

DOI: 10.1007/s00704-004-0041-z · Source: OAI

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Theor. Appl. Climatol. 78, 5–26 (2004)
DOI 10.1007/s00704-004-0041-z

1
Alterra, Wageningen University and Research Centre, Wageningen, The Netherlands
2
INPA, Manaus, AM, SP, Brazil
3
UFRA (formerly FCAP), Bel
em, PA, Brazil
4
Department of Atmospheric Sciences, IAG=University of S~ao Paulo, SP, Brazil
5
Federal University of Rond^
onia (UNIR), Ji-Paraná, RO, Brazil
6
Centre for Ecology and Hydrology, Wallingford, UK
7
Free University (VU), Amsterdam, The Netherlands

Comparative measurements and seasonal variations

in energy and carbon exchange over forest and pasture
in South West Amazonia
C. von Randow1, A. O. Manzi2 , B. Kruijt1 , P. J. de Oliveira3 , F. B. Zanchi4;5 ,
R. L. Silva5 , M. G. Hodnett6 , J. H. C. Gash6 , J. A. Elbers1 , M. J. Waterloo7 ,
F. L. Cardoso5 , and P. Kabat1

With 13 Figures

Received May 15, 2003; revised August 11, 2003; accepted August 28, 2003
Published online April 20, 2004 # Springer-Verlag 2004

Summary values) in the pasture compared to the forest. The night-

Comparative measurements of radiation flux components
and turbulent fluxes of energy and CO2 are made at two
sites in South West Amazonia: one in a tropical forest
reserve and one in a pasture. The data were collected from
February 1999 to September 2002, as part of the Large
Scale Biosphere-Atmosphere Experiment in Amazonia
(LBA). During the dry seasons, although precipitation and
specific humidity are greatly reduced, the soil moisture
storage profiles down to 3.4 m indicate that the forest vege-
tation continues to withdraw water from deep layers in the
soil. For this reason, seasonal changes observed in the
energy partition and CO2 fluxes in the forest are small,
compared to the large reductions in evaporation and photo-
synthesis observed in the pasture. For the radiation balance,
the reflected short wave radiation increases by about 55%
when changing from forest to pasture. Combined with an
increase of 4.7% in long wave radiation loss, this causes an
average reduction of 13.3% in net radiation in the pasture,
compared to the forest. In the wet season, the evaporative
fraction (
E=Rn) at the pasture is 17% lower than at the
forest. This difference increases to 24% during the dry
season. Daytime CO2 fluxes are 20–28% lower (in absolute
time respiration in the pasture is also reduced compared to
the forest, with averages 44% and 57% lower in the wet and
dry seasons, respectively. As the reduction in the nocturnal
respiration is larger than the reduction in the daytime
uptake, the combined effect is a 19–67% higher daily
uptake of CO2 in the pasture, compared to the forest. This
high uptake of CO2 in the pasture site is not surprising,
since the growth of the vegetation is constantly renewed,
as the cattle remove the biomass.
1. Introduction
An increasing number of observations and model
results show that Amazonian forest has a key
influence on the regional and global climate sys-
tem. The forest generates a major part of global
land surface evaporation (Choudhury et al.,
1998), and plays a prominent role in the atmo-
spheric carbon balance (Malhi et al., 1999; Keller
et al., 2001). Several measurement projects are
6 C. von Randow et al.
now underway measuring the spatial and inter-
annual variability in energy, water and carbon
fluxes from Amazonian forest – the objective is
to calibrate basin-wide modelling schemes so that
accurate estimates and predictions of these
exchanges can be made. The fluxes are being mea-
sured using the eddy correlation method, as it
provides direct, high time-resolution data repre-
senting the energy and gas exchange for the whole
ecosystem, over several square kilometres.
The eddy correlation technique was used in
campaign mode by the pioneering studies
of Amazonian forest evapotranspiration of
Shuttleworth et al. (1984) and Fitzjarrald et al.
(1988), and of carbon exchange of Fan et al.
(1990) and Grace et al. (1995). More recently, it
has been used by the flux community to study
seasonal response and annual budgets of canopy
carbon assimilation and forest respiration (Malhi
et al., 1998; Araujo et al., 2002; Miller et al.,
2003; Vourlitis et al., 2003). These studies have
significantly improved the understanding of the
response of the forest ecosystem to environmental
conditions. However, most of these long term flux
studies focus on primary forest, and little attention
is paid to the impacts of changes in surface vege-
tation cover. To assess the effects of these changes
requires comparative measurements over differ-
ent vegetation covers. Keller et al. (2003) have
recently highlighted some interesting differences
in the seasonal variability of carbon exchange
across Amazonia, which provides additional
motivation for comparative studies of the fluxes
in different regions of Amazonia.
The Bowen ratio (), the ratio of the sensible
(H) and latent (
E) heat fluxes, is a critical influ-
ence on the hydrological cycle, through its role in
boundary layer development, weather and cli-
mate. This influence is emphasised by various
modelling studies (e.g. Viterbo and Beljaars,
1995; Dickinson et al., 1991; Garratt, 1993)
which have shown that the performance of atmo-
spheric models depends on an accurate represen-
tation of these surface processes. In Amazonia, a
few studies with short term measurements (e.g.
Shuttleworth et al., 1984; Sá et al., 1998), and
recently with two one-year datasets, in central
(Malhi et al., 2002) and eastern Amazonia
(Rocha et al., 2003) have discussed the energy
partition and the controls on the seasonal varia-
tion of these fluxes. These studies have been
focused on forest areas; although Wright et al.
(1992, 1996) and Grace et al. (1998) have studied
the fluxes from Amazonian pasture there has
been relatively little consideration of the possible
impacts of land use changes.
Conversion of tropical forest in Amazonia to
pasture and agricultural plantations may lead to
impacts on the regional ecological, climatologi-
cal and hydrological processes. The climatic
and hydrological effects of possible Amazonian
deforestation were the main subject of the
Anglo-Brazilian Amazonian Climate Observa-
tion Study (ABRACOS; Gash et al., 1996). The
main results of ABRACOS indicate large poten-
tial impacts on regional climate, such as a reduc-
tion of up to 20% in precipitation and an increase
of 2
C on surface temperature (Nobre et al.,
1996). Other comparative studies show that net
radiation over forest areas is higher than in pas-
ture areas, due to differences in the reflected
solar radiation (albedo) and in the long wave
radiation balance (Bastable et al., 1993; Culf
et al., 1996). One deficiency of these studies is
that they only had independent measurements of
the short wave components of the radiation bal-
ance, estimating the long wave radiation balance
from the residual of the net radiation.
Recognising the need to better understand the
surface processes, of the radiation, energy and
carbon balances over forest and deforested areas
in Amazonia, in February 1999 two of the former
ABRACOS field sites in the Brazilian state of
Rond^onia were reactivated, as part of the Large
Scale Biosphere-Atmosphere Experiment in
Amazonia (LBA), one in the Biological Reserve
of Jaru (henceforth referred to as Rebio Jaru), an
area of little disturbed rainforest vegetation, and
one in the Fazenda Nossa Senhora ranch (FNS), a
large grassland ranch, about 80 km away. Mea-
surements of short and long wave radiation, heat,
water and CO2 fluxes were made almost continu-
ously from February 1999 to September 2002 at
these two sites. This paper highlights the differ-
ences and seasonal variability in the surface
energy and carbon exchange at these sites with
their two contrasting vegetation covers: tall trop-
ical forest and short grassland. We discuss the
differences in the short wave and long wave
radiation, in the energy partition between sensi-
ble and latent heat fluxes and in the carbon fluxes
at the two sites, both in the wet and dry seasons.
 Comparative measurements and seasonal variations 7

2. Site descriptions 1977, and, since 1991, has consisted of a homo-

geneous sward of perennial grass, with Brachiaria
Rebio Jaru is a terra firme forest area located
brizantha (A. Rich.) Stapf. as the dominant spe-
about 100 km north of Ji-Paraná, Rond^onia,
cies. At this site, a 5 m tower set up in 1991 was
Brazil. It consists of around 268000 ha of undis-
used during ABRACOS. In early 1999, another
turbed tropical forest and is located between
tower (8 m tall) was built 70 m away from the ori-
10
050 S and 10
190 S and 61
350 W and
ginal one, to support the LBA measurements. A
61
570 W, with altitude varying between 100
separate mast of 4 m was also set up to support the
and 150 metres above sea level. The canopy
flux instruments. There is sufficient uniform fetch
has a mean height of 35 m. However some of
for 1–2 km in all directions. Details of the vegeta-
the higher trees reach heights up to 45 m.
tion at both the Rebio Jaru and FNS sites are given
Andreae et al. (2002) give details of the vegeta-
by McWilliam et al. (1996).
tion at this site. At the end of 1998, a 60 m tower
Rond^onia state, in the south west part of
was built at this site (10
4.7060 S; 61
56.0270 W,
Amazonia does not suffer large influences either
at the height of 145 m A.S.L.), as part of two
of the sea or of topography, and the average tem-
subprojects: LBA=WETAMC (first LBA major
perature is almost constant throughout the year.
wet season Atmospheric Mesoscale Campaign,
However, a few cold fronts sometimes penetrate
Silva Dias et al., 2002) and LBA=EUSTACH
into the far north of the South American conti-
(European Studies on Trace gases and Atmo-
nent during June–July, causing the so-called
spheric Chemistry, Andreae et al., 2002). An
‘‘friagem’’ events, when relatively low tempera-
extra mast of 2.7 m was built later at the top of
tures may be observed. While the predominant
this tower.
climate is equatorial, warm and moist, the precip-
Although the forest reserve is protected by
itation varies strongly with seasons. The south-
the Brazilian Environmental Protection Agency
ern hemisphere summer is the rainiest period in
(IBAMA), in recent years it has been suffering
the region, with monthly totals over 200 mm. In
some small scale slash and burn activities, espe-
contrast during the dry season from June to
cially close to its north-western border, where it
August, it is common to observe several weeks
is relatively vulnerable to invasions by landless
without rain.
people. However, the few disturbed areas in the
sector from northwest clockwise to south–south-
east, the predominant wind direction, are very 3. Description of measurements
small, compared to the extensive areas of pristine and instruments
forest. Nevertheless, in the remaining sectors the
Several measurements were made continuously
undisturbed fetch is shorter, of the order of 1 km.
at both sites from the beginning of the activity
The River Ji-Paraná forms the western boundary
in early 1999. The instruments, data acquisition
of the reserve. On the other side of the river the
and power supply systems are nearly identical at
rain forest has been progressively cleared during
both sites and are briefly described in this sec-
the last 25 years. In summary, we can consider
tion. A full list of the measurements and instru-
the fetch to be predominantly undisturbed rain-
ments used on both sites is given in Table 1.
forest, however we should keep in mind that the
Automatic weather stations (AWS) composed
heterogeneity may cause important disturbances
of commercial sensors were installed on the
in the wind and scalar fields. The surface hetero-
towers and provided averaged measurements of
geneity of the area is observed not only because
the usual weather variables every half hour.
of contrasting deforested areas close by, but also
Measurements of soil moisture were also made
due to a few hills near the tower. The closest hill
weekly at both sites, using a neutron probe
is about 2 km northeast of the tower.
(Model IH, Didcot Instr. Co., UK). Measure-
The pasture site is located in the cattle ranch
ments were made at 0.2 m depth intervals to a
Fazenda Nossa Senhora (FNS), at 10
450 S and
maximum depth of 3.6 m in 6 access tubes (loca-
62
220 W, 293 m above sea level, near the town
tions) in the pasture and in 8 tubes in the forest.
of Ouro Preto D’Oeste, about 50 km from Ji-
In the pasture the measurements could be made
Paraná. This area was first deforested by fire in
to a depth of 3.6 m in all tubes, but in the forest,
8 C. von Randow et al.

Table 1. List of measurements, instruments and measurement heights for the automatic weather station and eddy correlation
instrumentation installed on Rebio Jaru (forest) and FNS (pasture) sites in Rond^
onia

Meteorological Used instrument, Heights

variables manufacturer (model)
FNS (pasture) Rebio Jaru (forest)

Incident and reflected Pyranometers Kipp & 6.5 m 19.3 m

short wave radiation Zonen (CM21)
Incident and emitted Pyrgeometers Kipp & 6.5 m 19.3 m
long wave radiation Zonen (CG1)
Photosynthetically Active Quantum sensor LI-COR 9.0 m 25.6 m
Radiation (PAR) (LI-190SZ)
Air temperature Vaisala thermohygrometer 8.3 m 60.0; 45.2; 35.0;
(HMP35A), PT100 resistors 25.3; 15.3; 5.3 m
Relative humidity Vaisala thermohygrometer 8.3 m 60.0 m
(HMP35A)
Wind speed Cup anemometers Vector A100R 9.3 m 61.1; 45.2; 34.7; 25.3 m
Wind direction Wind vane Vector (W200P) 9m 60.7 m
Rainfall Rain gauge EM ARG-100 0.5 m 60.3 m
Surface radiative Infrared sensor Heimann (KT15) 8.0 m 59.1 m
temperature
Atmospheric pressure Barometer Vaisala (PTB100A) 5.4 m 40 m
Temperature of PT100 resistors 6.5 m 54.3 m
pyrgeometers
Vertical profile of CO2 and Infrared gas analyser PP – 62.7; 45.0; 35.0;
water vapour concentration Systems (CIRAS SC) 25.0; 2.7; 0.05 m
Soil heat flux Flux plates Hukseflux (SH1) 1 and 5 cm 1 and 10 cm (depth)
(depth)
Soil temperature profile Soil thermometers IMAG-DLO 0.01; 0.05; 0.1; 0.05; 0.15; 0.3; 0.6;
(MCM101) 0.4; 1.0 m (depth) 1.0 m (depth)
Soil moisture profile FDR sensors IMAG-DLO 0.01; 0.05; 0.1; 0.05; 0.15; 0.3; 0.6;
(MCM101) 0.4; 1.0 m (depth) 1.0 m (depth)
Soil moisture profile with Neutron probe Every 20 cm down Every 20 cm down
Neutron probe to 3.6 m (depth) to 3.6 m (depth)
High frequency measurements Eddy correlation system 4.0 m 62.7 m
of 3-D wind speed, temperature, (Gill Sonic Anemometer and
H2O and CO2 concentration LI-COR 6262 IRGA)
(10.4 Hz)
 Height above canopy top (35 m)
 Vertical profiles of temperature, wind speed, water vapour and CO concentrations are installed only in the forest site
2
 Soil moisture profiles with neutron probe measured once a week

the maximum depth of measurement varied from
2.0 m to 3.6 m, because of the presence of hard
weathered bedrock in the profile. This led to an
important difference in the soil moisture storage
behaviour at the two sites; in the forest, water
draining from the profile in the wet season ponds
on the underlying bedrock, creating saturated
conditions, which may extend to within 1 m of
the surface during very wet periods. The ponded
water drains downslope towards the Ji-Paraná
river. Such saturated conditions rarely occurred
in the pasture.
Both sites were equipped with an eddy corre-
lation system, similar in design to the systems
described by Moncrieff et al. (1997). These are
closed-path systems, composed of a three axis
sonic anemometer (Solent 1012R2, Gill Instru-
ments, UK) and a fast-response (0.1 s response
time) infrared gas analyser (IRGA, LI-6262,
LICOR, USA). The air is drawn through a
 Comparative measurements and seasonal variations
4 mm internal diameter Teflon tube, 5 m in
length, from an inlet near the sonic to the IRGA,
using a membrane air pump (KNF, Germany)
at a flow rate of about 7 L min1 . The distance
between the inlet tube and the centre of the sonic
anemometer transducer array is about 20 cm. To
prevent dust entering the sample tubing, air filters
of 1 mm pore were used (ACRO 50, Gelman,
USA). In this setup, the H2O and CO2 mixing
ratio analogue signals output by the IRGA were
fed into the sonic anemometer in-built A=D con-
verter. These signals plus temperature and wind
velocities measured by the sonic were then
recorded at a rate of 10.4 Hz for later off-line flux
calculations, using the Alteddy software (Elbers,
1998). Alteddy was written in FORTRAN
language and can be adapted to a number of dif-
ferent hardware configurations and software
options. For our sites, the program was set to
compensate the time delay of the IRGA signals
and include corrections for instrument responses
and damping of fluctuations through the IRGA
tube, following the methodology described by
Moncrieff et al. (1997) and Aubinet et al.
(2000). Generally, these corrections are small
and represent an almost negligible uncertainty
factor to the final values (Kruijt et al., 2003).
Although the signals from the IRGA are cor-
rected for analyser cell temperature and pres-
sure, cross sensitivity and band broadening,
zero and span calibrations are frequently neces-
sary. Since the calibrations need to be done in
the field and as these are relatively remote sites
(especially the forest site), the instruments were
recalibrated at intervals of about 2 months. Very
little drift in the calibration values was ob-
served, usually smaller than 1% in the span of
the IRGA. Therefore, the effect on the calcu-
lated fluxes is almost negligible.
At the forest site, additional CO2 and H2O con-
centrations inside and above the canopy were
measured at six heights up the tower, using a slow
response infrared gas analyser (CIRAS SC, PP
Systems, UK), in the first one and a half year
period of measurements. This IRGA was stable
because the single analysis cell was thermostati-
cally controlled and zeroed on a half-hourly basis
with a chemically scrubbed air circuit.
The whole set of instruments and data acquisi-
tion systems is low power consuming and is pow-
ered by batteries, recharged using solar panels.
9
The set-up is very similar to the one used by
another LBA forest site: the ‘‘K34’’ site, near
the city of Manaus. Araujo et al. (2003) give a
more detailed description of these systems.
Despite the very careful, weather proof and
low-power design, there have been several break-
downs in different parts of the system, leading to
temporary or permanent replacement of some
sensors and causing a few gaps in the dataset.
Especially during the first two years, serious prob-
lems happened at both sites. In the forest site, a
lightning strike on the tower damaged most of
the sensors. In the pasture site, a faulty sonic
could only be replaced several months after the
detection of the problem. For these reasons the
flux data coverage during 1999–2000 was lim-
ited, with fluxes available for 62% of the time
in the forest and only 42% in the pasture. The
data coverage during the period 2001–2002 is
much better, about 86% and 84%, in the forest
and pasture sites, respectively. The AWS data
coverage is generally very good, covering 92–
99% of the time in both sites.
4. Results and discussion
4.1 Flux data processing and energy
balance closure
The fluxes of sensible heat, water vapour and
CO2 were estimated using the eddy correlation
method. The fluctuations of the variables were
calculated by subtracting 30 minute block aver-
age values (or up to 8 hours in a low frequency
study) from the instantaneous measurements.
Also, two rotations were applied to align the
coordinate frame with the mean streamlines and
to force the mean vertical component ( w) to zero
(McMillen, 1988). The averaging and rotation
period used defines the main scales of motion
that contribute to the calculated transport of the
scalars, acting as a filter for low frequencies. The
large heterogeneity of the terrain is therefore
likely to add large uncertainties associated with
low frequency contributions to the fluxes. For
example, the energy balance closure at the forest
site is very poor, as shown in Fig. 1. This figure
presents hourly values of the sum of the sensible
(H) and latent (
E) heat fluxes against the ‘‘avail-
able’’ energy A. The term A is calculated as
A ¼ Rn  G, where Rn is the net radiation and
10 C. von Randow et al.
Fig. 1. Sum of sensible and latent heat fluxes plotted
against the available energy for half-hourly measurements
made during 1999. The available energy is calculated by
subtracting the soil heat flux and the heat storage in canopy
air space and biomass from the net radiation
G is either the soil heat flux, in the pasture, or the
sum of the soil heat flux and the heat storage in
the canopy air space and biomass, calculated
using the parameterisation proposed by Moore
and Fisch (1986), in the forest. A large imbalance
is shown in this figure. The energy balance clo-
sure over the pasture site (not shown) is usually
better, but still it is not always achieved (the sum
of the fluxes in the pasture range from 80 to
110% of available energy).
The analysis shown in Fig. 1 include the angle
of attack dependent calibration described by Gash
and Dolman (2003) and Van der Molen et al.
(2003). These authors examined the effect of the
angle of attack (the angle that the wind vector
makes with the horizontal axis of the sonic) dis-
tribution on sonic anemometer-based flux mea-
surements. Gash and Dolman (2003) found that,
for a forest site, more than 50% of the daytime
fluxes were carried by eddies with angles of attack
that were outside the manufacturer’s recom-
mended operating envelope. Van der Molen et al.
(2003) measured the response of two types of
sonic anemometer in a wind tunnel experiment
and derived angle of attack dependent corrections.
We applied these corrections to a few days of
Rebio Jaru data. On average, the re-calibration
increases the sensible heat fluxes by 8.2% and
the latent heat fluxes by 7.1%.
Even after correcting for the angle of attack on
the sonic anemometer, there is still a shortfall of
26% in the energy balance closure at the Rebio
Jaru site and the reasons are unclear. Several
other studies have reported similar discrepancies
between measured fluxes and available energy
(Twine et al., 2000). This lack of energy closure
reduces the usefulness of the eddy correlation
data for model validation or parameter calibra-
tions. A careful analysis of the possible sources
of uncertainty is thus necessary.
There has been much recent discussion about
the uncertainties and possible errors in flux mea-
surements using the eddy correlation technique
over complex surfaces (Mahrt, 1998; Lee,
1998; Finnigan, 1999; Sakai et al., 2001;
Finnigan et al., 2003; Kruijt et al., 2003). In sum-
mary, apart from errors related to instrument lim-
itations, several distinct factors that contribute to
the variability of surface exchange processes add
complications to the estimation of the fluxes in
the region by the eddy correlation method, such
as: (i) mesoscale circulation induced by horizon-
tal heterogeneity of the terrain; (ii) non-station-
ary conditions and disturbed boundary layers
associated with strong convective events present
in Amazonia; (iii) the effects of slow wind direc-
tion changes in complex topography terrain that
are likely to modulate the stream flows; and (iv)
especially for carbon budget studies, the horizon-
tal advection of scalars in stable conditions. Over
the Rebio Jaru forest, von Randow et al. (2002)
showed that a substantial amount of the
exchanges of mass and energy between the forest
canopy and the atmosphere occur due to meso-
scale motions, which might not be taken into
account if the fluxes were calculated using the
usual short-averaging periods procedures. Kruijt
et al. (2003), reviewing the sources of uncertain-
ties on all the processing steps of calculations of
fluxes from the raw turbulent data, also pointed
out the high sensitivity of the estimations to the
treatment of low frequencies and non-horizontal
flow in the region. All these problems might, to
some extent, explain the apparent underestima-
tion of heat fluxes (lack of energy balance clo-
sure) and very large observed annual carbon
uptake rates (usually not in agreement with eco-
logical expectations, Malhi and Grace, 2000).
For carbon dioxide fluxes, there is the additional
problem of poor nighttime mixing leading to
potential advective losses. This effect is not
likely to significantly affect energy fluxes as
these are generally very small during nighttime.
Nevertheless, even subject to possible large
 Comparative measurements and seasonal variations
uncertainties in the absolute accuracy, the eddy
correlation method is considered a powerful tool
when used for analyses of temporal trends (sea-
sonal or inter-annual variations, for instance),
since the uncertainties in the absolute accuracy
of the flux measurements are thought not to vary
too much between seasons.
Finnigan et al. (2003) showed that the proce-
dure to rotate the coordinate frame to be aligned
with the streamlines, acts as a high pass filter for
the covariances, such that the contributions from
fluctuations over periods longer than the aver-
aging period are lost. This suggests that the rota-
tions should only be applied on a long time scale
basis. To analyse whether that is the reason the
energy fluxes at the forest are apparently under-
measured we performed a study reprocessing the
data collected over the forest site for 48 days
augmenting the averaging time periods up to 8
hours. Figure 2 shows the variation of the energy
balance closure (represented as the ratio of the
sum of heat fluxes to the available energy) with
the period used to calculate the mean and fluctu-
ating parts of the turbulent fluxes. The result is
similar to the analysis for data collected near
Manaus (central Amazonia) shown in figure 14
of Finnigan et al. (2003), with the energy balance
closure increasing as the averaging time is
increased from 15 minutes to 2 hours, while
further increase of the period out to 8 hours has
only a small effect on closure. However the main
difference is that, at Rebio Jaru, the energy bal-
ance closure does not reach the 100% level. Both
at Manaus and at Rebio Jaru, deep moist convec-
tion allows very large convective motions to
develop within the boundary layer. Sufficiently
Fig. 2. Ratio of heat fluxes to available energy at Rebio
Jaru for different averaging and rotation periods
11
far above the ground, therefore, we can expect
substantial low frequency contributions to the
covariances. In that sense, at both sites the high
measurement heights allow these slow motions to
impact on the measured fluxes. At Rebio Jaru,
however, the terrain is more complex: not only
is the terrain not flat (there are a few hills in the
surroundings of the tower, but there are also large
deforested areas to the south and west of the
reserve. Regardless of the predominant wind
direction from the north and eastern sectors, the
contrasting surface vegetation covers may induce
mesoscale circulations that modulate the turbu-
lent transports (Von Randow et al., 2002). For
this reason, even when the averaging and coordi-
nate rotation is extended so that all the low
frequency contribution to the vertical transport
is captured, steady horizontal flux divergences
may still contribute to the total balance and these
cannot be estimated from measurements made on
a single tower (Finnigan et al., 2003).
We conclude that the lack of energy balance
closure at our sites is the result of one or both the
following reasons:
(i) transports on time scales longer than 8 hours
are still significantly contributing to the total
exchange. As a result of slow wind direction
changes there still may be a low frequency
component that we are not able to capture
using short time rotation scales;
(ii) a significant amount of the energy is trans-
ported horizontally over the region by local
circulations causing horizontal flux diver-
gences. Unfortunately, it is simply not pos-
sible to estimate this component from
measurements made on a single tower.
A new experiment is needed to specifically
investigate the spatial variability at this site. This
experiment should include a detailed investiga-
tion of the interactions of flow with the region
topography and vegetation cover, at a range of
time scales.
Hereafter we concentrate on comparative mea-
surements over the two contrasting types of sur-
face, rather than on the methodological issues. As
discussed by Twine et al. (2000), by independently
measuring the net radiation, the heat fluxes at the
soil surface and the energy storage in the biomass
and canopy air space, the heat fluxes can be
adjusted in two ways: either simply discarding
12
the latent heat measurements and estimating this
component as the residual of the energy balance or
adjusting both the sensible and latent heat flux
maintaining the ratio between them (Bowen ratio)
as measured by the eddy correlation system.
Applying the first procedure is justifiable if it is
assumed that H is accurately measured, but
E is
likely to be more subject to uncertainties in the
measuring device (in our case, the closed-path
IRGA) than H (calculated only from the sonic
measurements). The alternative method of adjust-
ing both fluxes, keeping the measured Bowen
ratio, is more appropriate when it is likely that
the underestimation of the fluxes are caused not
by the instrument limitations, but because of a fail-
ure to capture low frequency transport or advec-
tion. In the literature, both approaches are used
(Twine et al., 2000) and we have also decided to
adjust the fluxes in both ways. This approach pro-
vides a range of values for the fluxes, instead of
just one weakly defensible method.
4.2 Meteorological conditions
and soil moisture storage
This and subsequent sections present the results
of several aspects of the data. Comparisons are
made between the measurements over the pasture
and forest sites and between wet and dry season
periods.
Monthly averages of air temperature and spe-
cific humidity and monthly totals of rainfall mea-
sured over the pasture (FNS) and forest (Rebio
Fig. 3. Monthly averages of air temperature (circles), specific humidity (inverted triangles) and monthly totals of precipitation
(columns) measured over the forest (represented by closed symbols) and the pasture (represented by open symbols), from
February 1999 until September 2002
C. von Randow et al.
Jaru) sites during the period February 1999 to
September 2002 are shown in Fig. 3. The mean
air temperature shows some variability between
months, but the differences are very small, rang-
ing only between 22 and 27
C and it is not easy
to identify a clear seasonal pattern. A few low
temperature events seem to drive the averages
down in some years in January–February, prob-
ably related to strong precipitation situations, and
in June–July, due to the influence of the so-called
‘‘friagens’’ (the cold fronts that can penetrate far
north in the continent during these months). On
the other hand, a clear drop in specific humidity
and a drastic reduction in rainfall during the dry
seasons is observed, at both sites. Surprisingly,
through almost the entire period of observations,
the rainfall amounts were much higher in the
forest, where annual amounts ranged from 2000
to 2400 mm, than in the pasture, where the mea-
surements indicated about 1400–2000 mm of
rainfall per year. Although previous studies indi-
cate a reduction in the precipitation over pasture
compared to forest areas, when the current data
are compared with previous data collected during
ABRACOS (Hodnett et al., 1996), the differ-
ences are much higher in this current data. It is
not possible to say whether this large difference
is real or an artefact of inaccurate measurements
in one or both of the sites. The specific humidity
is also always higher in the forest area, with aver-
age values ranging from 15.8 g kg1 in the dry
seasons to 17.5 g kg1 in the wet seasons, while
in the pasture the average values are 13.4
 Comparative measurements and seasonal variations
and 16.0 g kg1 in the dry and wet seasons,
respectively.
In addition to the specific humidity, the speci-
fic humidity deficit is also of interest. Figure 4
shows monthly average values of specific humid-
ity deficit in g kg1 , over the forest and pasture
sites. As expected, it clearly shows that the def-
icit is consistently greater at the pasture site than
over the forest. This figure also highlights the
strong seasonality effect on air humidity at both
sites.
The drastic reduction in humidity and, more
importantly, in precipitation, has impacts on the
soil water storage behaviour. Figure 5 shows the
storage of water for the layers from 0–2 m and
2–3.4 m in the soil profile, for both forest and
pasture (It should be noted that the storage values
are the equivalent depth of water in the profile,
based on the soil moisture determined by drying
the soil in an oven at 105
C. The values give no
indication of water availability).
The storage in the 2–3.4 m layer in the forest
remained constant in the wet season, indicating
that the profile was saturated. The very high stor-
age in the 0–2 m layer in March 2000, January
13
Fig. 4. Monthly averages of specific hu-
midity deficit measured over the forest
(closed circles) and the pasture (open cir-
cles), from February 1999 until Septem-
ber 2002
Fig. 5. Storage of water in the soil at for-
est and pasture sites, for the layers from
(a) 0–2 m and (b) 2–3.4 m deep
2001 and January 2002 was the result of the satu-
rated conditions extending upward to less than
1 m below the surface. This is not seen in the
pasture. At the start of the dry season, the rate
of moisture storage change in the forest is very
rapid compared to that in the pasture, because the
profile is losing water by root uptake (to supply
transpiration), and by lateral drainage.
The data for both forest and pasture show a
very pronounced seasonal cycle, but the seasonal
changes are very much larger in the forest than
the pasture, in the upper and lower layers shown.
In the lower profile, the seasonal change was
about 110 mm in the pasture compared to about
290 mm in the forest. In the pasture, the largest
decreases of storage in the lower profile occurred
at the end of the wet season and in the early dry
season, and were mainly due to drainage. In the
pasture, during July 2001, the rate of moisture
loss from the upper profile was 2.26 mm d1
compared to only 0.45 mm d1 from the lower
profile. For the forest, the rates of moisture loss
for the same period were 1.82 mm d1 and
1.64 mm d1 respectively, giving a total of
3.46 mm d1 . The rate of loss from the upper
14 C. von Randow et al.

layer in the pasture was higher than that of the
forest in this period, but this probably reflects the
fact that the forest had already used a greater
proportion of the available water from this layer.
The loss rates for the lower profile show a large
contrast, with little root uptake from below 2 m
in the pasture, compared to the forest.
In the forest, in the upper layer, the minimum
storage reached in each of the four dry seasons
shown was very similar. This indicates that the
limit of water availability was being reached. In
the pasture, the minimum storage reached varied
between the four seasons, with more uptake in
1999 and 2002 compared to in the other dry sea-
sons. In the forest it was of note that uptake in the
lower layer ceased soon after the storage in the
upper layer had increased following rainfall
inputs. This can be seen by comparing the forest
curves in Fig. 5a and b. The storage in the lower
layer decreases during all dry seasons (Fig. 5b),
but as soon as an increase is observed in the
upper layer (Fig. 5a), usually in the beginning
of September, a levelling in the lower layer is
noted. As the rainfall inputs continue through
the wet season the water storage is largely
increased in both layers.
4.3 Radiation balance
The net radiation (or radiation budget) at the sur-
face is described by:
Rn ¼ ðSin  Sout Þ þ ðLin  Lout Þ ð1Þ
which is the summation of short wave and long
wave radiation components: incident (Sin) and
reflected (Sout) solar radiation; and incident
(Lin) and emitted (Lout) terrestrial radiation. All
of the components, especially the upward ones
may present differences over different vegetation
covers, and also between wet and dry season per-
iods. To assess these, two composites represent-
ing wet and dry season periods were calculated,
averaging the measurements each half hour for
all of the components. For the wet season com-
posites, data between January and March were
used, whenever available within the 4 years

Fig. 6. Top panels: average daily patterns of incident solar radiation (Sin, circles), reflected solar radiation (Sout, inverted
triangles) and net radiation (Rn, diamonds), during (a) wet season and (b) dry season. Measurements at forest are represented
with closed symbols and at pasture, with open symbols. Bottom panels: same as top panels, but for incident (Lin, squares) and
emitted (Lout, triangles) terrestrial radiation, during (c) wet and (d) dry season periods
 Comparative measurements and seasonal variations
Table 2. Average values of radiation components in W m2 , over forest and pasture sites. The absolute differences between
pasture and forest measurements are represented by P-F, and the percentage, calculated by these differences divided by the
measurements at the forest, represent the relative effect of changing the surface from forest to pasture vegetation cover. Ln is the
net longwave radiation, defined as the difference between Lin and Lout
Sin Sout
Forest 206.0 26.1
Pasture 202.8 40.6
Land use change effect
P-F 3.2 14.5
(P-F)=F (%) 21.6 155.5
studied. For the dry season composites, data
between July and September were used. Since
the data coverage is usually very good for all
the radiation components, it is likely that these
composites are good representatives of the aver-
age conditions during wet and dry season
periods.
The daily patterns of the radiation compo-
nents, provided by the wet and dry season com-
posites, are presented in Fig. 6. From these
figures we can compare the behaviour of each
component over the two types of surface and
during the wet and dry seasons. First, comparing
the measurements over the two sites (comparing
the curves with closed and open symbols), inci-
dent solar radiation is slightly higher over the
forest than in the pasture, as shown in Fig. 6a
and b. From the same figures it can also be seen
that the solar radiation reflected by the pasture
vegetation is higher than the forest. The average
long wave components, shown in Fig. 6c and d,
also present some interesting features. Incident
long wave radiation (square symbols on Fig. 6c
and d) is more or less similar over the two sites,
although there is an indication that it is slightly
higher in the pasture in the wet season. The out-
going terrestrial radiation, on the other hand,
shows marked differences between the two types
of surface, being significantly higher during day-
time over pasture, but with similar values during
night time. Since it is mainly dependent on the
surface temperature, this reflects the effect of
higher diurnal temperature variation observed in
the pasture (Culf et al., 1996). The result, mainly
driven by a larger daytime loss, is that the long
wave radiation budget is larger (more negative)
in the pasture than in the forest area. The com-
bined effect of higher reflectivity (albedo) and
higher daytime long wave emission in the pasture
15
Lin Lout Rn Albedo Ln
411.6 448.0 143.2 0.13 36.3
413.6 451.6 124.2 0.20 38.0
2.0 3.7 19.0 0.07 1.7
10.5 10.8 213.3 157.9 14.7
cause a large difference between the net radiation
over the two surfaces. In both seasons, the net
radiation is much higher in the forest than in
the pasture.
Table 2 presents the average values of all the
radiation components in W m2 , over the two
sites. To quantify the effect on the radiation com-
ponents of changing the vegetation cover from
rainforest to a cattle ranch, the absolute differ-
ences between pasture (P) and forest (F) mea-
surements and the percentage, calculated by
these differences divided by the measurements
at the forest, are also presented. It can be seen
that the most important change occurs in the
reflected short wave radiation, which increases
by about 55% when changing from forest to pas-
ture. Combined with an increase of 4.7% in long
wave radiation loss, this causes an average reduc-
tion of 13.3% in the net radiation.
Comparing the different characteristics
between the two seasons, it is interesting to
notice that the main differences are observed in
the downward components. That is, the most pro-
nounced changes are in the components related
to the transfer from the atmosphere to the surface
(incident radiation). The upward components
(solar radiation reflected and terrestrial radiation
emitted by the surface) have more or less similar
values in the two season composites (Fig. 6a and
b). The seasonal differences in incident solar
radiation may be caused by larger cloud cover
during the wet season, but probably lessened by
the effect of burning activities that are very fre-
quent during the dry season and cause strong
smoke pollution over the whole region. As we
can see comparing Fig. 6a and b, the high cloud-
iness during the wet season reduces the average
incident solar radiation more than the smoke in
the dry season. On the other hand, the incident
16 C. von Randow et al.
Fig. 7. Monthly averages of albedo over forest (closed
circles) and pasture (open circles) during 1999–2002
long wave radiation, largely affected by the
humidity in the atmosphere, is notably lower in
the dry season than in the wet season (Fig. 6c and
d), at both sites. Because of this, even with the
surface emitting more or less the same amount of
terrestrial radiation in both seasons, the long
wave loss is slightly higher (more negative) in
the dry season, both in the pasture and in the
forest. Therefore the short wave balance, higher
in the dry season (Fig. 6a and b) competes with
the long wave balance, higher in the wet season
(Fig. 6c and d). As noticed comparing Fig. 6a
and b, the net all wave radiation is higher in
the dry season, therefore more influenced by
the short wave component.
Concerning the seasonal variations and the dif-
ferences in albedo between the sites Culf et al.
(1995) and Culf et al. (1996) presented detailed
discussions, using data collected from 1991 to
1993, during ABRACOS project. Our data show
similar results, summarised as follows. Figure 7
shows monthly average values of albedo for data
collected at Rebio Jaru and FNS sites, during
1999–2002. The seasonal variation at the forest
site is evident, with the highest values occurring
at the same time as the driest soil moisture
conditions. At the pasture the monthly variation
is not well correlated with soil moisture, and, as
discussed by Culf et al. (1995), the pasture
albedo does not have a regular seasonal cycle,
probably because the overall albedo measured
is a combination of the reflectance from both
the grass and from the bare soil. The decrease
that might be expected during the wet season
appears to be offset by the higher albedo of
new grass growth. Combining with data from
other pasture areas, Wright et al. (1996) showed
that the albedo there is related to the leaf area
index.
To better visualise the seasonal variations on
the net radiation budget, Fig. 8 presents monthly
averages of the net shortwave balance (Sn ¼
Sin  Sout), net long wave balance (Ln ¼ Lin 
Lout), and net all-wave radiation (Rn). It is noted
that, although the long-wave components play a
role, the variability of net radiation is mainly
driven by the short wave balance. Malhi et al.
(2002), using a slightly different analysis for a
forest area in central Amazonia, concluded that
the long-wave balance was a more important
determinant of seasonal variations of the net
Fig. 8. Monthly averages of radiation bal-
ances of shortwave radiation (Sn ¼ Sin 
Sout, circles), longwave radiation (Ln ¼
Lin  Lout, squares) and net all-wave radia-
tion (Rn, inverted triangles), over forest
(closed symbols) and pasture (open
symbols)
 Comparative measurements and seasonal variations 17

Fig. 9. Average daily patterns of net radiation (Rn), sensible and latent heat fluxes (H and
E respectively) and soil heat fluxes
(þ heat storage in canopy at forest), for: (a) wet season at forest; (b) wet season at pasture; (c) dry season at forest and (d) dry
season at pasture. Dashed areas represent the ranges of heat fluxes calculated using two different procedures (see Section 4.1)

radiation, than the albedo. However they anal-
ysed the variations by normalising the com-
ponents by the incident solar radiation. That
way, they highlighted that the surface reflection
(albedo) is not as important to the seasonal
variability of net radiation as the long wave
balance. In this context our results are not in
disagreement, as it was previously shown that
there was little variation in the outgoing short
wave.
4.4 Sensible and latent heat fluxes
In a similar way to the wet and dry season com-
posites for the radiation components, the average
daily patterns of sensible and latent heat fluxes
over forest and pasture were calculated and are
presented in Fig. 9, together with the curves of
net radiation. In the case of the pasture, the soil
heat flux (G) is also included, as measured by 4
flux plates buried close to the surface (1 cm). For
the energy balance in the forest area, the change
in energy storage in the canopy air space and
biomass is significant and these fluxes were
added. This ‘‘storage term’’ was estimated by
the parameterisation according to changes in air
temperature and humidity changes inside the
canopy proposed by Moore and Fisch (1986).
For both the sensible and latent heat fluxes,
instead of one curve with the average values, a
range of curves are presented, limited by the two
methods of energy balance closure forcing: (i)
replacing the
E measurements by the residual
of the energy balance; or (ii) adjusting both H
18 C. von Randow et al.
and
E fluxes to maintain the measured Bowen
ratio. Analysing the impact of the dry season at
both sites (comparing the top panels, (a) and (b),
with the bottom ones, (c) and (d)) it is clearly
seen that very little change is observed in the
forest while larger changes occur in the pasture.
In the forest, the fluxes are slightly higher during
the dry season, due to a small increase in the net
radiation, but relative changes in the energy par-
tition are hardly seen in this figure. In the pasture,
on the other hand, while the evapotranspiration
rates are reduced, the sensible heat flux is largely
increased. These differences are explained by the
fact that the forest trees, with deep roots, can
maintain a large uptake of soil water even after
a long dry period, as seen by the soil water stor-
age records (Fig. 5). Comparing Fig. 9b and d, it
is also interesting to note that the range of flux
uncertainty in the pasture is higher during the wet
season. As discussed by Garstang and Fitzjarrald
(1999, pp. 285–287), in the presence of strong
convection activity and precipitating clouds, the
boundary layer in the tropics presents complex
inter-scale links. These ‘‘disturbed’’ boundary
layers have qualitatively different characteristics
than are observed in undisturbed boundary
layers, and the occurrence of strong updrafts
and outflows make a large contribution to the
exchange processes in the surface-atmosphere
interface. Von Randow et al. (2002) showed that,
during the wet season, the boundary layer over
the region is indeed largely influenced by such
processes. This may explain the higher uncer-
tainty in the flux calculations during the wet
season.
From the separate wet and dry season compo-
sites, the averages and the differences between
these averages of the sensible and latent heat
fluxes are presented in Table 3. The values,
Table 3. As in Table 2, but for average values of sensible and latent heat fluxes calculated during wet and dry season periods.
The evaporative fraction (
E=Rn) is also shown
Wet season
Rn H
E
Forest 136.1 31.6 104.5
Pasture 128.6 45.5 83.0
Land use change effect
P-F 7.5 13.9 21.5
(P-F)=F (%) 25.5 144.2 220.5
presented in W m2 , are the averages of the
fluxes adjusted for energy balance closure main-
taining the measured Bowen ratio. The differ-
ences between the two sites obtained by
adjusting the
E as the residual are of similar
amounts. As expected, large differences between
the two types of surface are noticed. In the pas-
ture, the sensible heat fluxes are 28–45% higher
while the evapotranspiration rates are 20–41%
lower. In the wet season the evaporative fraction
(
E=Rn) in the pasture is 17% lower than in the
forest. This difference is increased to 24% during
the dry season.
To better visualise these differences on energy
partition over the two vegetation covers and
between the seasons, Fig. 10 presents the evolu-
tion of the monthly variation of the Bowen ratio
at both sites. The top curves (triangles facing up)
are the values calculated from the heat fluxes
measured directly by the eddy correlation sys-
tem; the bottom curves (triangles facing down)
are the Bowen ratios obtained after calculating
the latent heat fluxes as the residual of the energy
balance; and the middle curves (circles) represent
the average between the two. The Bowen ratio
varies little over the year in the forest, with
values ranging from 0.3 to 0.4, although a slight
increase can be seen at the end of the dry season
(Fig. 10a). In the pasture, a large seasonality is
observed (Fig. 10b), with the Bowen ratio chang-
ing from 0.3–0.6 in the wet season to 0.6–0.8,
again highlighting the effect of water stress dur-
ing the dry season.
4.5 Net Ecosystem Exchange of CO2
The Net Ecosystem Exchange (NEE) of carbon
dioxide between the forest and the atmo-
sphere can be estimated by combining the flux
Dry season

E=Rn Rn H
E
E=Rn
0.77 146.9 38.3 108.6 0.74
0.64 113.0 49.1 63.9 0.56
0.13 33.9 10.8 44.7 0.18
216.9 223.1 128.1 241.2 224.3
 Comparative measurements and seasonal variations 19

Fig. 10. Monthly averages of Bowen ratio ( ¼ H=
E) as measured from the eddy correlation system (triangles), calculated
after estimating
E by the residual of the energy balance (inverted triangles), and the average between the two cited methods
(circles), at (a) forest and (b) pasture

measurements from the eddy correlation with
profile measurements of CO2 concentration
below the flux sensors. The NEE is calculated
as the sum of the fluxes measured at the top of
the tower and the change in storage of CO2 in the
layer below (Lee, 1998; Grace et al., 1995).
ð data were available, according to the amount of
dC
NEE ¼ Fc þ Mc dz ð2Þ
dt
where Fc is the flux of CO2 measured by the
eddy correlation and the second term is the stor-
age of CO2 (Mc is the molar weight of carbon
and dC=dt is the change in CO2 concentration
between several heights).
In practice, the storage term is calculated by
approximating the derivatives as finite differ-
ences between two successive measurements
and the integrals by weighted sums of the vari-
ables at the 6 levels. After June 2000 the profile
system broke down and no direct measurements
of the flux due to change in storage were then
available. To estimate this flux after this period
the following procedure was employed: using the
14 months of data of concentration profiles avail-
able we first calculated the average storage flux
at each time of day separating the data into three
classes depending on the friction velocity (u )
averaged on the night before (or current, for
nighttime data) of the measurement. These
classes are when average night-time u ranges
between (i) 0 and 0.1 m  s1 , (ii) 0.1 and
0.2 m  s1 and (iii) higher than 0.2 m  s1 . These
stratified storage values were then used as a
lookup table to substitute the storage when no
turbulence observed during the preceding (or cur-
rent, for nighttime data) night. The quality of this
empirical CO2 storage model was tested by with-
holding data during 10 days that presented a
range of different weather conditions and com-
paring the NEE calculated using the empirical
model against the measurements. The results
are shown in Fig. 11. Although the model is very
simple, the results were considered satisfactory
for the purpose of this paper.
No other corrections were applied to the NEE
estimates, despite several recent papers indicat-
ing that the interpretation of nocturnal measure-
ments is the largest single source of uncertainty
in the absolute accuracy of daily or annual totals
of carbon exchange in the tropical forests
(Araujo et al., 2002; Kruijt et al., 2003; Miller
et al., 2003). This is due to the fact the NEE is a
relatively small difference between two large
quantities: the uptake of CO2 due to photosyn-
thesis during daytime, referred to as the Gross
20 C. von Randow et al.

Fig. 11. Net ecosystem exchange esti-

mated using the empirical CO2 storage
model (see Section 4.5) plotted against
measurements (calculated with mea-
sured CO2 concentration profiles), for
10 days in 1999. The 1:1 line is also
shown

Primary Production (GPP) and the release by the
ecosystem respiration (Reco). This way, a small
day to night bias on NEE measurements, such as
an inability to measure CO2 advection during
calm nights, may create large errors in the annual
budget. In an attempt to account for this possible
night time loss, several researchers plot nighttime
NEE measurements against u and filter out the
data when a reduction of respiration is seen dur-
ing low u conditions (Miller et al., 2003). Kruijt
et al. (2003) showed, however, that no clear
reduction was seen at the Rebio Jaru site, using
the data collected during the first year of
measurements (see Fig. 9d of Kruijt et al.,
2003). For this reason, and since our aim here
is to concentrate on the relative differences in
CO2 exchange among the sites (and the seasonal
patterns), no further corrections were applied to
the data.
Figure 12 shows the NEE values averaged
according to classes of incident Photosyntheti-
cally Active Radiation (PAR), for wet and dry
season periods, measured at Rebio Jaru (Fig.
12a) and at FNS (Fig. 12b). Figure 12a shows
that the ecosystem light responses at the forest
show the typical behaviour of initial strong

Fig. 12. Net ecosystem exchange of CO2 (NEE) averaged according to classes of Photosynthetically Active Radiation (PAR),
for data collected during dry and wet seasons at the forest (a) and pasture (b)
 Comparative measurements and seasonal variations
Fig. 13. Daily patterns of NEE for both sites, during wet (a) and dry (b) seasons
decrease (increase of uptake) with PAR, saturat-
ing at a PAR of about 1000 mmol m2 s1 , for
both periods. The shape of these curves is very
similar to that reported for other forest areas in
Amazonia (Malhi et al., 1998; Carswell et al.,
2002; Goulden et al., 2003). A small reduction
in the initial slope and in the maximum assimila-
tion is observed in the dry season curve. The
NEE curve for the wet season period saturates
at about 23 mmol m2 s1 , while for the dry
season it reaches about 20 mmol m2 s1 . For
the pasture site, the differences between the wet
season and the dry season light responses are
much bigger. In the wet season, the typical
near-linear light response of the C4 grasses is
evident, whereas in the dry season fluxes are
strongly reduced after the PAR becomes higher
than 1000 mmol m2 s1 , with average saturation
values of 10 mmol m2 s1 , and the light
response curve is not linear. This reflects the fact
that the carbon assimilation by the pasture vege-
tation is strongly affected by a reduction in soil
moisture content. These large differences on the
seasonal variability observed at the two sites are
mainly explained by the ability of the forest to
avoid severe drought stress by extracting the
water from deep layers in the soil (Fig. 5).
Figure 13 presents the average daily patterns
of CO2 fluxes over the two sites, during wet and
dry season periods. The fluxes present the typical
patterns of vegetated areas, with negative fluxes
during the day (photosynthesis activity higher
21
than respiration) and positive fluxes during the
night (respiration activity only). There is also a
noticeable reduction in the fluxes at both sites
during the dry season. Although there is a small
reduction in the respiration, a bigger effect on the
daytime fluxes causes a reduction in the NEE
(less uptake) in the dry season. It is interesting
to compare this pattern at Rebio Jaru with other
sites in the Amazon Basin. Vourlitis et al. (2003)
also found for a transitional forest (ecotonal
between rainforest and savanna) that the most
negative NEE occurred during the rainy season.
At two sites, near Manaus (Araujo et al., 2002)
and Caxiuana (Carswell et al., 2003), little
seasonal variation was observed, while near
Santar
em (Goulden et al., 2003) a higher uptake
was measured during the dry season. The latter
pattern appears to be driven by a strong decrease
in respiration during the dry season, without a
comparable reduction in photosynthetic activity.
Understanding what controls the seasonal differ-
ences across sites is an essential component of
LBA. Access to deep soil water may vary across
sites and, additionally, innate phenological con-
trols may play an important role in the regulation
of seasonal carbon uptake (Keller et al., 2003).
It is also interesting to notice in Fig. 13 that
the daytime fluxes are very similar at both the
forest and pasture sites during the afternoon,
but lower (higher uptake) in the forest in the
morning. In the pasture the daytime evolution
is more or less symmetric around the negative
22
peak at noon, while at the forest the fluxes are
clearly different in the morning and afternoon
hours. This decline in afternoon fluxes was also
reported for other forest sites in Amazonia
(Malhi et al., 1998; Goulden et al., 2003).
Goulden et al. (2003) showed, for a forest site
in eastern Amazonia, that this afternoon decline
is not correlated to the soil water content, and
indeed, if that were the case, we would expect
the pasture site to present a similar response.
Measuring the stomatal conductance of several
tree species in Rebio Jaru during ABRACOS,
McWilliam et al. (1996) did not find a correlation
between the stomatal conductance and light
intensity (although they argue that this may be
due to poor sample size), air temperature or leaf
water potential, but they found a good correlation
with the vapour pressure deficit. However, during
a ‘‘friagem’’ event, the authors also considered the
possibility of an internal circadian rhythm con-
trolling stomatal closure of some species. There-
fore, the afternoon decline in photosynthesis
is probably caused by forest stomatal closure
responding to high vapour pressure deficit, but
a circadian rhythm may also play a role. Compar-
ing nighttime fluxes, we notice that the respira-
tion rates are much higher in the forest,
averaging 6 to 9 mmol m2 s1 , while at the pas-
ture they reach only 3 to 5 mmol m2 s1 through-
out the night.
The average differences between the NEE mea-
sured at the forest and pasture are presented in
Table 4. It is interesting to compare our measure-
ments with previous measurements at the Rebio
Table 4. Average values of Net Ecosystem Exchange measured over the two sites during daytime (08:00–18:00 h), nighttime
(19:00–05:00 h), peak photosynthesis activity, and daily totals
Wet season
2 1
mmol m s mmol m2 s1
Daytime Nighttime Daytime
peak
Forest 14.4 8.1 22.4
Pasture 11.2 4.5 17.2
Land use change effect
P-F 3.1 3.6 5.2
(P-F)=F (%) 121.9 244.5 123.3
 Note that this increase is related to negative values (uptake by photosynthesis), therefore indicate a decrease in the productivity
C. von Randow et al.
Jaru site shown by Grace et al. (1995). Those
authors used measurements collected during 11
days in the dry season of 1992 and 44 days in the
wet season of 1993 to fit a process-based model.
They then used the model to estimate that the
forest absorbed, on average, 8.5 mol C m2 year1
(that would represent an average of about
2.8 kg C ha1 day1 ). The values of daily totals
measured during 1999–2002 shown in Table 4
suggest rates 4 to 6 times bigger. Both datasets
indicate little evidence of nighttime losses during
calm nights (Grace et al., 1996; Kruijt et al.,
2003a; Kruijt et al., 2003b), but the uptake rates
implied from 1999–2002 data are still very high
and considered implausible by many ecologists.
Since there are no other physiological measure-
ments available at the site to support the eddy
correlation measurements, it is still not clear
why the forest at Rebio Jaru seems to absorb that
much carbon from the atmosphere.
Comparing the fluxes at the forest and pasture,
large differences are noticed. During the wet sea-
son, the daytime averages, calculated with data
collected between 08:00 and 18:00 L.T., are 22%
higher (less negative) in the pasture. The higher
daytime fluxes actually indicate less photosynthe-
sis activity at the pasture. The nighttime respira-
tion is also reduced compared to the forest, with
averages 44% lower. During the dry season, these
differences increase: 28% less photosynthesis
and 57% less respiration are observed in the pas-
ture compared to the forest. As the reduction in
the nocturnal respiration is higher than the reduc-
tion in the daytime uptake, the combined effect
Dry season
Daily total Daily total
(kg C ha1 Daytime Nighttime Daytime (kg C ha1
day1 ) peak day1 )
18.3 10.5 7.1 17.5 8.3
21.8 7.6 3.0 13.2 13.8
3.5 3.0 4.1 4.3 5.6
219.2 128.3 257.4 124.7 267.5
 Comparative measurements and seasonal variations
is a 19–67% higher daily uptake of CO2 in the
pasture, compared to the forest. This high uptake
in the pasture site is not surprising, since the
growth of the vegetation is constantly renewed,
while the cattle remove the biomass. As dis-
cussed before, one other important factor that
may add a large uncertainty on these numbers
is the effect of drainage of CO2 during stable
conditions that may not be accounted for. In
the pasture site, especially during the dry season,
a very stable layer is frequently observed at
night, and, under these situations, even a very
small slope in the terrain may cause a significant
drainage loss, therefore these results should be
viewed with caution.
5. Conclusions
In this work we present the data of radiation flux
components and turbulent fluxes of energy and
CO2 collected almost continuously from Febru-
ary 1999 to September 2002 in two different sites
in south western Amazonia: one in a forest
reserve (Rebio Jaru) and one in a pasture cattle
ranch (FNS). Comparisons are made between the
measurements over the two sites and between
wet and dry season periods.
The energy balance closure at the forest site is
poor: the sum of the turbulent fluxes reaches only
about 74% of the available energy. At the pasture
the energy balance closure is better, but still not
always achieved. The reasons for the apparent
underestimation of the turbulent fluxes are still
unclear and may be related to two factors: (i)
slow wind direction changes on undulating ter-
rain in the region, adding a significant low
frequency component that we are not able to
capture using short time scale rotations; (ii) hor-
izontal flux divergences that are simply not pos-
sible to estimate from measurements made on a
single tower. To concentrate on the comparative
measurements over the two contrasting types of
vegetation cover, we adjusted the turbulent fluxes
in two ways: calculating the latent heat flux as
the residual of the energy balance or adjusting
both the sensible and latent heat flux to maintain
the Bowen ratio as measured by the eddy corre-
lation system.
While the temperatures present little variation
between the seasons, the specific humidity and
precipitation amounts are greatly reduced during
23
the dry season periods (June to September), com-
pared to the measurements during wet season
(December to March) at both sites. Comparing
the two sites, large differences are observed
in precipitation, specific humidity and specific
humidity deficit.
Changes in soil moisture storage profiles give
indications of the uptake of water by the vegeta-
tion and the drainage at the two sites. The pasture
vegetation withdraws water only from the upper
layers of the soil with the water stored in the
layer from 2 to 3.4 m deep showing only little
variation, mainly caused by drainage. In the
forest, on the other hand, the soil water storage
changes more rapidly in this layer – the seasonal
change was about 290 mm in the forest and
110 mm in the pasture. These large variations
in the forest are partly caused by lateral drainage,
but also give an indication of the ability of forest
vegetation to uptake water from deep layers in
the soil.
The radiation flux components are markedly
different between the two sites. The most impor-
tant changes occur in the reflected short wave
radiation, which increases about 55% when chang-
ing from forest to pasture. Combined with an
increase of 4.7% on long wave radiation loss, this
causes an average reduction of 13.3% in the net
radiation in the pasture, compared to the forest.
Seasonal changes at both sites are observed
mainly in the incident radiation (short and long
wave), driving large seasonal variations in the net
radiation. Although the long-wave components
play a role, the variability of net radiation is
shown to be mainly driven by the short wave
balance.
Large differences between the two types of
surface are also noticed in the energy partition
between sensible and latent heat fluxes. In the
wet season the sensible heat fluxes are 45%
higher, while the evapotranspiration rates are
20% lower in the pasture, compared to the forest.
In the dry season, the differences are lower in the
sensible heat (fluxes are 28% higher in the pas-
ture), while the changes in evapotranspiration are
large (rates are 41% lower in the pasture). In the
wet season the evaporative fraction (
E=Rn) at
the pasture is 17% lower than at the forest. This
difference increases to 24% during the dry sea-
son. Analysing the seasonal variations we ob-
served that the Bowen ratio is relatively constant
24 C. von Randow et al.
over the forest, varying between 0.3–0.4,
although a slight increase was observed in the
end of the dry season. At the pasture site, on
the other hand, a large variation was observed,
with the Bowen ratio changing from 0.3–0.6 in
the wet season to 0.6–0.8 in the dry.
Light response curves of the net ecosystem
exchange of CO2 were analysed with data
from the two sites for wet and dry seasons.
The NEE at the forest show the typical be-
haviour of initial strong decrease (increase of
CO2 uptake) with increasing PAR, saturating at
20 to 23 mmol m2 s1 at a PAR of about
1000 mmol m2 s1 . A small reduction in the
initial slope and in the maximum assimilation
was observed in the dry season curve. For the
pasture site, the differences between the wet
season and the dry season light responses are
much bigger. In the wet season, the typical
near-linear light response of the C4 grasses is
observed, whereas in the dry season fluxes are
strongly reduced after the PAR becomes higher
than 1000 mmol m2 s1 , with average saturation
NEE of 10 mmol m2 s1 . Differences in day-
time NEE between the two sites are then larger
in the dry season: daytime productivity is about
28% lower in the pasture in the dry season,
while this difference is about 20% in the wet
season. The nighttime time respiration in the
pasture is also reduced compared to the forest,
with averages 44% and 57% lower in the wet
and dry seasons, respectively. As the reduction
in the nocturnal respiration is higher than the
reduction in the daytime uptake, the combined
effect is a 19–67% higher daily uptake of CO2
in the pasture, compared to the forest. This high
uptake in the pasture site is not surprising, since
the growth of the vegetation is constantly
renewed, as the cattle remove the biomass.
Acknowledgements
Firstly, many thanks are due to all of the great number of
people who worked in the field data collection, maintenance
and logistics, without them this work would have never been
possible. We also gratefully acknowledge the support of
IBAMA, INCRA and UNIR, Ji-Paraná. Special thanks also
go to Afonso Pereira de Andrade, owner of Fazenda Nossa
Senhora (FNS) and to IBAMA Rebio Jaru co-ordination, for
giving us permission to work in the reserve and use their
facilities. The research was supported under the overall LBA
framework, and financed by the European Union (FP5
EUSTACH and CARBONSINK projects) and by the Bra-
zilian agencies Conselho Nacional de Pesquisa e Desenvolvi-
mento Tecnol
ogico (CNPq) and Fundac° ~ ao de Amparo  a
Pesquisa do Estado de S~ ao Paulo (FAPESP). C. von
Randow’s PhD research project is currently financed by the
CAPES (Brazil) and WOTRO-NWO (Netherlands) agencies.
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Authors’ addresses: C. von Randow (e-mail: Celso.
vonrandow@wur.nl), B. Kruijt, J. A. Elbers, P. Kabat, Alterra,
Wageningen University and Research Centre, PO Box 47,
NL-6700 AA Wageningen, The Netherlands; A. O. Manzi,
INPA, Manaus, AM, Brazil; P. J. de Oliveira, UFRA
(formerly FCAP), Bel
em, PA, Brazil; F. B. Zanchi, Depart-
ment of Atmospheric Sciences, IAG=University of S~ao
Paulo, SP, Brazil; R. L. Silva, F. L. Cardoso, Federal Uni-
versity of Rond^onia (UNIR), Ji-Paraná, RO, Brazil; M. G.
Hodnett, J. H. C. Gash, Centre for Ecology and Hydrology,
Wallingford, OX10 8BB, UK; M. J. Waterloo, Free University
(VU), Amsterdam, The Netherlands.