Communications in Soil Science and Plant Analysis, 45:2970–2978, 2014

Copyright © Taylor & Francis Group, LLC

ISSN: 0010-3624 print / 1532-2416 online
DOI: 10.1080/00103624.2014.956937

Variations in the Diurnal Flux of Greenhouse Gases

from Soil and Optimizing the Sampling Protocol
for Closed Static Chambers

MATTHEW K. D. HALL, ANTHONY J. WINTERS,

AND GORDON S. ROGERS
Faculty of Agriculture and Environment, University of Sydney, Sydney,
Australia

There is no standardized method for the sampling of greenhouse gas fluxes from soil.
Two methods are primarily used: closed dynamic chamber (CDC) and closed static
chamber (CSC) systems. The most complex and costly are the CDC systems, which can
sample gases in situ. However, the low-cost CSC systems are being increasingly used
in which the gas samples are collected manually and analyzed off-site at a later date.
Given their growing popularity, it is important to optimize the sampling procedure of the
CSC systems to ensure that the measurements are both repeatable and representative.
Samples from a commercial potato crop were collected in the morning and afternoon at
0, 15, 30, 60, 90, and 120 min after the chambers were closed, and the concentrations of
carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) were determined using
gas chromatography. The concentrations of CO2 and N2 O inside chambers increased
linearly over time, whereas the concentration of CH4 remained constant. The fluxes of
CO2 and N2 O from soil were greater in the afternoon than the morning, whereas the flux
of CH4 was greater in the morning. For longer-term single-point soil flux monitoring
using CSCs with a volume of 6.3 L, it is recommended that samples are collected in
the morning at 0, 30, and 60 min after chambers are closed. This approach will ensure
that the concentration of the gases are representative and will allow for a high level of
repeatability and certainty in the results.

Keywords Environmental monitoring, gas sampling, global warming, methodology,

mitigation, protocol, soil respiration

Introduction
Greenhouse gases (GHGs) have the capacity to absorb and emit thermal radiation. The
increased release of these gases into the atmosphere by human activities means that our
decisions have the capacity to influence global ambient temperatures. The three GHGs of
interest from an agricultural perspective are carbon dioxide (CO2 ), methane (CH4 ), and
nitrous oxide (N2 O). The release of these gases from farming systems is higher than other
land uses, due to the greater inputs of fertilizer and water (Smith et al. 2008; Burney, Davis,
and Lobell 2010). The emission of GHGs from agricultural land continues to be a focal
point for mitigation strategies by land-management agencies. To evaluate the effective-
ness of different land-management strategies on the release of these gases, first scientists
Received 5 January 2014; accepted 30 May 2014.
Address correspondence to Matthew K. D. Hall, Faculty of Agriculture and Environment,
University of Sydney, Sydney, Australia. E-mail: matthew.hall@sydney.edu.au

2970
 Variations in the Diurnal Flux of Greenhouse Gases 2971

must be able to accurately quantify their release from environmental systems. In spite of
this effort, the methodology for the sampling and measurement of GHGs varies greatly,
which can in turn influence the emission estimates (Juszczak et al. 2009; Heinemeyer and
McNamara 2011). It is important to establish a standardized methodology for the sam-
pling of these gases from land used for agricultural production in order to improve the
accuracy and transparency of gas measurements and facilitate comparisons between GHG
measurements of different studies.
The most common methods of measuring GHG fluxes from the soil are through the
use of either a closed dynamic chamber (CDC) or closed static chamber (CSC) system.
Closed dynamic chamber systems measure the flux of gases in situ and are able to operate
continuously and autonomously. This system eliminates the need to store samples prior
to analysis, reducing errors associated with sample transfer and time lapse between col-
lection and measurement (Rochette and Eriksen-Hamel 2008; Parkin and Venterea 2010).
However, the CDC system is the most expensive and technically complex to operate and
is limited by the number of treatments that can be imposed (Willey and Chameides 2007;
Farkas et al. 2011). Additionally, the gas chromatography (GC) instrument(s) used to quan-
tify these gases are only physically able to measure a certain number of samples, as they
are unable to store samples long term and are restricted by sample run times (Ball, Scott,
and Parker 1999).
The use of CSCs circumvents this problem because the number of chambers is only
limited by the amount of manual labour available. Some of the basic considerations for
sampling using CSCs have been proposed such as their general design, sampling pro-
cedures, and sample storage and handling (Cleemput and Boeckx 2005; Rochette and
Eriksen-Hamel 2008; Farkas et al. 2011). However, none of these studies have recom-
mended a methodology supported by the investigation of how the fluxes of all three GHGs
change over time. Usually, studies focus on optimizing the measurement of only one GHG.
The advantages and limitations of the various methods used to measure soil CO2 fluxes
have been discussed in depth by Liang et al. (2004), yet very few studies have examined
the changes in the diurnal flux of CH4 and N2 O using CSC systems. The present study
aims to identify a protocol for the simultaneous measurement of all three GHGs.
The procedures used to measure GHG fluxes from soil vary greatly between studies,
particularly the amount of time that the chambers are closed, which ranges from a few
minutes to a few hours (Willey and Chameides 2007). For the CSC systems, 30 min is rec-
ommended as sufficient time for the chambers to accumulate gases, with multiple sampling
points during this period (Cleemput and Boeckx 2005; Farkas et al. 2011). Heinemeyer and
McNamara (2011) have shown that the sample accumulation time has a profound effect on
the calculated flux of CO2 . This is due to the asymptotic increase in the concentration of
CO2 over time; because of this, a shorter accumulation time of approximately 15 min was
proposed.
The time of day during which samples are collected varies greatly between studies;
Parkin and Venterea (2010) recommended that the time of flux measurement should corre-
spond closely with the daily average temperature, such as the midmorning or early evening.
These periods of sample collection are supported by Ma et al. (2013), who have shown that
CO2 fluxes from soil increase from around 0600 h to a peak flux at around 1300 h. This
response supports the concept of sample collection during temperature stable periods of
the day, as the flux of CO2 is more stable and representative of the daily average during
these periods. These times of the day are optimal if single-point measurements are taken
over longer periods of time, such as long-term environmental monitoring. This diurnal
2972 M. K. D. Hall, A. J. Winters, and G. S. Rogers

response of CO2 flux is likely due to the temperature dependency of microbial turnover
of soil carbon and nitrogen (Schaufler et al. 2010; Frey et al. 2013). Hence, the release of
gases by this process may be more consistent and representative of the daily average during
temperature stable periods of the day, such as the midmorning and early evening.
The concentration of the gases in samples are most commonly determined using GC,
but an infrared gas analyser (IRGA) can also be used to measure CO2 , particularly for
CDC systems (Farkas et al. 2011). The concentrations are usually extrapolated to an area
per unit time basis, such as flux ha−1 year−1 ; however, the problem with this is that the
accumulation of gases inside a chamber does not follow a 1:1 linear relationship with
the progression of time. Hence, the amount of time that chambers are closed for has a
profound impact on the calculated flux of these gases from soil. The present study sought
to determine the optimal sampling times for the three GHGs using a CSC system. It is
important to propose a unified sampling protocol for the measurement of GHG fluxes from
soil using CSCs in order to improve comparisons between different studies.

Materials and Methods

Location of Field Experiments

The experiments were completed on a commercial farm, 80 km southwest of Sydney, at
Theresa Park, New South Wales, Australia (33.98◦ S, 150.64◦ E). At this location the
mean temperature during the experiment ranged from 16 to 28 ◦ C (Australian Bureau of
Meteorology, Camden airport, station number 068192, distance ∼5 km). Irrigation was
provided by a lateral-move irrigation system. The potato plants were grown using stan-
dard 0.9-m row widths, with 30 cm spacing between the plants. The variety of potato was
Atlantic, a typical-yielding crisping variety. The crop was subjected to the normal crop
management practices used on this farm, and no treatments were imposed.

Experimental Design
Four CSCs were randomly located in a commercial potato crop. The crop was at growth
stage III (tuber initiation) when sampling commenced. The edge of the chamber was
pushed into the soil to a depth of approximately 8 cm (Parkin and Venterea 2010). Gas
samples were collected during the summer, in December 2010 and January 2011. The
chambers were exposed to the open air until the time of sampling, upon which they were
closed by applying the lid. Chambers had a 4-mm vent tube near the ground level, allow-
ing the pressure to equalize when they were closed (Xu et al. 2006). The samples were
collected at 0, 15, 30, 45, 60, and 120 min after the chambers were closed.

Sample Collection
The chambers had an internal diameter of 24 cm and an approximate headspace volume
of 6.3 L. They were placed in the centre of a row over bare soil. The lid and rubber seal
were placed on the chambers and the samples were collected at different time intervals, in
the morning and afternoon, beginning at 1000 and 1400 h, respectively. These times were
chosen to avoid potential flux peaks caused by irrigation events and periods that closely
corresponded to the average daily temperature. Samples were collected across 5 days dur-
ing the period of measurement. At these sample collection events, a 25-ml gas sample was
 Variations in the Diurnal Flux of Greenhouse Gases 2973

collected and forced-filled into an evacuated 10-ml Exetainer (Labco Ltd., Lampeter, UK).
Samples were stored at ambient temperature until the analysis. Irrigation was not provided
to the crop at least 24 h before samples were collected.

Determination of Carbon Dioxide and Methane

An SRI Instruments (Torrance, Calif.) gas chromatograph (GC) with a thermal conductivity
detector (TCD) and flame ionization detector (FID) were used to determine the concentra-
tions of CO2 and CH4 , respectively. The TCD was operated at 130 ◦ C and the FID at
180 ◦ C. The oven temperature was held isothermally at 35 ◦ C, and an injection volume of
3 ml was used. The samples had a run time of 3.5 min and were separated using a Porapak
Q column (80/100, 6 ft × 1/8 in. × 2.1 mm, Sigma-Aldrich, Castle Hill, NSW, Australia).
The CO2 [746 ppm ± 15] and CH4 [1.5 ppm ± 0.1] concentrations in air (BOC Gases,
Sydney, Australia) were used to calibrate the instrument at the beginning and through-
out each measurement period. A five-point calibration curve was established by making
dilutions of these standard gases.

Determination of Nitrous Oxide

The concentration of N2 O in the samples was determined using a Shimadzu-8A (Shimadzu,
Kyoto, Japan) GC fitted with an electron capture detector (ECD) and a Porapak Q column
(80/100, 6 ft × 1/8 in. × 2.1 mm, Sigma-Aldrich, Castle Hill, NSW, Australia). The
column temperature was held isothermally at 70 ◦ C. A 0.3-ml gas sample was injected
onto the column with a run time of 5 min. The N2 O [0.5 ppm ± 0.1] concentration in air
(BOC Gases, Sydney, Australia) was used to calibrate the instrument at the beginning and
throughout each measurement period. A five-point calibration curve was established using
this standard gas.

Flux Calculations
Gas fluxes from soil were calculated using the equation published by Hutchinson and
Mosier (1981). This equation assumes that over time the flux of gases decrease as the
difference between the concentration gradient of the soil and headspace decrease [(Eq. (1)]:

f0 = (c1 − c0)2 / [t1 × (2 × c1 − c2 − c0] × In[ (c1 − c0/c2 − c1)] (1)

where f0 is the soil flux (nL L−1 h−1 ); c0, c1, and c2 are the chamber headspace gas
concentrations (nL L−1 ) at times 0, 1, and 2 respectively; and t1 is the interval between
sampling points (h).

Statistical Analysis
The data were analyzed using GenStat, 13th ed. (GenStat, Hemel Hempstead, UK).
Restricted maximum likelihood (REML) was used to analyze the data, with the accu-
mulation time and time of day analyzed as factors. Differences between the means were
determined using the least significant difference (5%).
2974 M. K. D. Hall, A. J. Winters, and G. S. Rogers

Results and Discussion

Influence of the Accumulation Time on the Headspace Concentration of GHGs

The concentrations of CO2 and N2 O inside a CSC were influenced by the accumulation
time and time of day when the samples were collected, but not the interaction between these
factors; the concentration of CH4 was not influenced by the accumulation time but rather
the time of day when the samples were collected. This indicates that very small amounts of
CH4 were released from the soil, illustrating that the simultaneous measurement of GHG
fluxes from soil is difficult, as a universal sampling protocol is unlikely to be optimal for
all GHGs.
The concentrations of CO2 and N2 O inside a CSC increased linearly over a 2-h period
(Figures 1 and 2). This linear increase in the headspace concentration of CO2 is much
longer than that reported in other studies (Cleemput and Boeckx 2005; Farkas et al. 2011),
where a peak in the asymptotic increase of CO2 is reported after approximately 15 min
(Heinemeyer and McNamara 2011). These differences between studies may be related to
differences in regional conditions and sample collection and analysis procedures. This dif-
ference between studies further illustrates the difficulties in proposing a universal sampling
protocol as local conditions such as soil type, soil usage, and environmental conditions all
influence the amount and behavior of soil GHG fluxes.
However, CSCs seem to be a cost-effective and efficient way of determining fluxes, as
a linear increase in the concentration of CO2 and N2 O over time was shown. This response
between accumulation time and concentration of the gases is similar to that reported by
Ball, Scott, and Parker (1999) and Farkas et al. (2011). The relationship between the con-
centration of these gases and the accumulation time means that there is good repeatability
of this system to measure CO2 and N2 O. This is possible as the headspace concentration
of these gases increases linearly over the tested time range, and that the response was
repeatable over multiple days of flux measurements.

Figure 1. Concentration of CO2 over time inside a closed static chamber. Bars represent the standard
error of the mean, P < 0.01, REML, n = 40.
 Variations in the Diurnal Flux of Greenhouse Gases 2975

Figure 2. Concentration of N2 O over time inside a closed static chamber. Bars represent the standard
error of the mean, P < 0.01, REML, n = 40.

In the case of CH4 flux, it is difficult to determine an optimal time for measurement
as the concentration remained constant during the period of measurement. The flux of this
gas from soil is generally lower from vegetable systems when compared to other farming
systems (Biswas et al. 2010; Denmead et al. 2010), particularly for frequently tilled soil
that does not receive the addition of manure from livestock. In this case, a headspace accu-
mulation time of 60 min is proposed, with samples collected at 0, 30, and 60 min after the
chamber is closed. This approach will provide accurate flux estimates for CO2 and N2 O as
these gases increase linearly over this time range; additionally it will also provide a rela-
tively long accumulation time for any potential CH4 fluxes to be captured. These sample
collection intervals provide a good compromise for the simultaneous measurement of all
three GHGs.

Influence of the Time of Day on GHG Fluxes

The concentrations of CO2 and N2 O were greater in the afternoon than in the morn-
ing, whereas the concentration of CH4 was greater in the morning than in the afternoon
(Table 1). This response further illustrates the difficulties associated with the simultane-
ous measurement of GHG fluxes over the same time period, as the flux responses of the
different gases are distinctly different and respond independently of each other.
Greater N2 O fluxes during the afternoon have also been reported by Jantalia et al.
(2008), who showed that the mean daily fluxes are greatest at approximately 1300 h, which
is similar to the time when the afternoon samples were collected in this experiment. Ham
et al. (1995) and Ma et al. (2013) have shown that CO2 fluxes are greater in the afternoon
than in the morning. This response is linked to increases in the ambient and soil temper-
atures, which result in greater fluxes caused by increases in microbial and root activity
(Smith et al. 2003). In comparison, the CH4 fluxes from soil decrease with prolonged
increases in the temperature (Wang, Neue, and Samonte 1997; Wu et al. 2010); which
2976 M. K. D. Hall, A. J. Winters, and G. S. Rogers

Table 1
Change in the concentration of greenhouse gases depending on the time of day
the samples are collected

Time of daya g CO2 m−3 µg CH4 m−3 µg N2 O m−3

Morning 2.67 bb 1300 a 384 b
Afternoon 2.95 a 1252 b 451 a
a
Samples were collected in the morning and afternoon starting at 1000 and 1400 h,
respectively.
b
Values in columns followed by the same letter are not significantly different by least
significant difference at 5%.

may be related to the methanotrophic oxidation of CH4 to CO2 in the soil surface layer
(Joabsson and Christensen 2002). These responses may explain why the fluxes of CH4 in
the present study were greater during the morning than the afternoon.
In vegetable cropping systems with high levels of soil cultivation and inputs, it is
preferable to take single-point measurements in the morning at around 1000 h. This time
of day for sample collection has three advantages. First, CH4 fluxes are greater during this
period of the day, meaning that the likelihood of capturing low fluxes is increased. Second,
for longer term environmental monitoring it is more consistent to collect samples under
temperature-stable periods of the day, such as the midmorning. Third, sampling at this
time of day will provide a strong confidence in the results, as the fluxes of CO2 and N2 O
are unlikely to be overestimated.

Conclusion
The results of this study show that the simple low-cost CSC systems are useful for simulta-
neously measuring GHG fluxes from the soil of vegetable cropping systems, but that there
are certain limitations to their use. The influence of these negative aspects can be reduced
by altering the sample collection techniques. Although a universal protocol is difficult to
propose for all experimental conditions, our results indicate that sample collection in the
morning after 0, 30, and 60 min will provide a good compromise for the simultaneous
measurement of all three GHGs. The results of this study indicate that a common method-
ology for sampling using static chambers is critical if realistic comparisons are to be made
between studies. Further research is necessary to develop a universal sampling protocol for
the simultaneous measurement of GHG fluxes under different environmental conditions.

Funding
This work has been funded by Horticulture Australia Limited (HAL) using voluntary con-
tributions from industry and matched funds from the Australian Government. This work
represents a component of Project VG09138: Quantifying the effects of no-till vegetable
farming and organic mulch on emissions and soil carbon.

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