Biogeosciences, 14, 1947–1967, 2017
www.biogeosciences.net/14/1947/2017/
doi:10.5194/bg-14-1947-2017
© Author(s) 2017. CC Attribution 3.0 License.
Methane exchange at the peatland forest floor – automatic chamber
system exposes the dynamics of small fluxes
Mika Korkiakoski1, Juha-Pekka Tuovinen1, Mika Aurela1, Markku Koskinen2, Kari Minkkinen2, Paavo Ojanen3,
Timo Penttilä3, Juuso Rainne1, Tuomas Laurila1, and Annalea Lohila1
1Finnish Meteorological Institute, Atmospheric Composition Research, P.O. Box 503, 00101 Helsinki, Finland
2University of Helsinki, Department of Forest Sciences, P.O. Box 27, 00014 University of Helsinki, Finland
3Natural Resources Institute Finland, Viikinkaari 4, 00790 Helsinki, Finland
Correspondence to: Mika Korkiakoski (mika.korkiakoski@fmi.fi)
Received: 2 June 2016 – Discussion started: 26 July 2016
Revised: 18 January 2017 – Accepted: 13 March 2017 – Published: 10 April 2017
Abstract. We measured methane (CH4) exchange rates with
automatic chambers at the forest floor of a nutrient-rich
drained peatland in 2011–2013. The fen, located in south-
ern Finland, was drained for forestry in 1969 and the tree
stand is now a mixture of Scots pine, Norway spruce, and
pubescent birch. Our measurement system consisted of six
transparent chambers and stainless steel frames, positioned
on a number of different field and moss layer composi-
tions. Gas concentrations were measured with an online cav-
ity ring-down spectroscopy gas analyzer. Fluxes were cal-
culated with both linear and exponential regression. The
use of linear regression resulted in systematically smaller
CH4 fluxes by 10–45 % as compared to exponential regres-
sion. However, the use of exponential regression with small
fluxes (< 2.5 µg CH4 m−2 h−1) typically resulted in anoma-
lously large absolute fluxes and high hour-to-hour deviations.
Therefore, we recommend that fluxes are initially calculated
with linear regression to determine the threshold for “low”
fluxes and that higher fluxes are then recalculated using ex-
ponential regression. The exponential flux was clearly af-
fected by the length of the fitting period when this period
was < 190 s, but stabilized with longer periods. Thus, we
also recommend the use of a fitting period of several minutes
to stabilize the results and decrease the flux detection limit.
There were clear seasonal dynamics in the CH4 flux: the for-
est floor acted as a CH4 sink particularly from early summer
until the end of the year, while in late winter the flux was very
small and fluctuated around zero. However, the magnitude
of fluxes was relatively small throughout the year, ranging
mainly from −130 to +100 µg CH4 m−2 h−1. CH4 emission
peaks were observed occasionally, mostly in summer dur-
ing heavy rainfall events. Diurnal variation, showing a lower
CH4 uptake rate during the daytime, was observed in all of
the chambers, mainly in the summer and late spring, partic-
ularly in dry conditions. It was attributed more to changes in
wind speed than air or soil temperature, which suggest that
physical rather than biological phenomena are responsible
for the observed variation. The annual net CH4 exchange var-
ied from −104± 30 to −505± 39 mg CH4 m−2 yr−1 among
the six chambers, with an average of−219 mg CH4 m−2 yr−1
over the 2-year measurement period.
1 Introduction
Methane (CH4) is one of the most important atmospheric
greenhouse gases due to its capability to absorb thermal
radiation and warm the climate (IPCC, 2014). One of the
main sources of CH4 globally is peatland (e.g., Denman et
al., 2007), where CH4 is produced by the decomposition
of organic matter in anaerobic conditions. Around 3 % (ca.
4 000 000 km2) of the Earth’s land surface is covered by peat-
lands (Clarke and Rieley, 2010) and the majority of these are
located in the boreal region (Fischlin et al., 2007). About one
third (104 000 km2) of European mire and peat resources are
located in Finland (Montanarella et al., 2006) and more than
half (55 000 km2) of this area has been drained for forestry
(Päivänen and Hånell, 2012).
Methane can be both produced and consumed in soil so
that the net CH4 flux depends on the rate of CH4 produc-
Published by Copernicus Publications on behalf of the European Geosciences Union.
1948 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
tion in anoxic soil layers and on the rate of CH4 oxidation in
the oxic soil layers. In peatlands, the thickness and depth of
CH4 producing and oxidizing layers are largely determined
by the water table (Bubier and Moore, 1994), which controls
the vertical distribution of oxygen in the soil profile. CH4 is
produced under anaerobic conditions by microbes known as
methanogens. The production rate is dependent on the avail-
ability of organic substrates at low redox potential (Eh) val-
ues and is controlled by soil temperature and pH (Dunfield et
al., 1993; Wang et al., 1993; Segers, 1998; Kotsyurbenko et
al., 2004). In contrast, oxidation of CH4 occurs in the oxic
soil layer closer to the surface and potentially also in the
moss layer (Larmola et al., 2010). Like the production rate,
the oxidation rate is controlled by soil temperature and pH
(Dunfield et al., 1993; Scheutz and Kjeldsen, 2004; Boeckx
and Van Cleemput, 1996), but many other factors also af-
fect oxidation processes, such as soil water content, soil tex-
ture, nutrients, and CH4 and oxygen concentration (Boeckx
and Van Cleemput, 1996; Ridgwell et al., 1999; Scheutz and
Kjeldsen, 2004). In addition to the direct control of produc-
tion and oxidation rates, there are other phenomena which
may affect the observed net CH4 flux above the soil surface,
including lateral CH4 transport in the soil (Christophersen
and Kjeldsen, 2001) and subsurface storage (Hutchinson et
al., 2000).
In environments with low soil CH4 production, such as
upland forest soils, grasslands, and tundra, uptake of at-
mospheric CH4 by the methanotrophic microbes dominates
(Dutaur and Verchot, 2007). This is also what commonly
happens after the drainage of peatlands, which results in
water level drawdown and increased oxic layer thickness.
Thereby, CH4 production is decreased and the fraction of
oxidized CH4 increased (e.g., Moore and Knowles, 1989;
Roulet et al., 1992). Consequently, the CH4 oxidation rate in
the aerated surface soil and mosses typically exceeds CH4
production that occurs deeper in the soil, thus turning in
particular well-drained peatlands into net CH4 sinks (Mar-
tikainen et al., 1995; Minkkinen et al., 2007; Ojanen et al.,
2010; Lohila et al., 2011). However, poorly drained sites may
remain to act as CH4 sources (Ojanen et al., 2010). In addi-
tion, the drainage ditches even at well-drained sites typically
continue to emit CH4 at rates similar to pristine boreal peat-
lands (Minkkinen et al., 1997; Minkkinen and Laine, 2006;
Luan and Wu, 2015).
Closed chambers are commonly used in the measurement
of greenhouse gas exchange between the forest floor and
the atmosphere (e.g., Denmead, 2008; Forbrich et al., 2010;
Koskinen et al., 2014). Unlike the eddy covariance (EC)
method, which is more suitable for measuring fluxes at the
ecosystem level, the chamber method permits the investiga-
tion of small-scale processes, such as the gas exchange of
different microtopographic surfaces, and enables the quan-
tification of spatial variation (Keller et al., 1990; Singh et
al., 1997). However, there are various details related to the
chamber design and the deployment of this measurement
technique in practice that may have a significant impact on
the flux that is estimated from the observed concentration
change in the chamber headspace. For example, the flux es-
timate seems to depend on the dimensions of the chamber
(Pihlatie et al., 2013). In addition, chambers should include
a fan to evenly distribute the air in the chamber headspace
(Pumpanen et al., 2004; Christiansen et al., 2011) although
the rotational speed of the fan should be kept low to avoid ex-
cessive turbulence (Koskinen et al., 2014). A major source of
uncertainty is the impact of the chamber itself on the gas con-
centration gradient in the soil (Healy et al., 1996; Hutchinson
et al., 2000; Conen and Smith, 2000; Davidson et al., 2002;
Livingston et al., 2005) and in the boundary layer just above
it. The concentration gradient is critical as it drives the soil–
atmosphere gas exchange and thus any aerodynamic distur-
bance may impact the observed flux.
The gradient between the soil and the air inside the cham-
ber changes when the gas concentration inside the cham-
ber changes during the measurement. This changes the flux,
which makes the concentration change nonlinear in time.
However, nonlinearity of the concentration during the cham-
ber closure may also result from chamber leaking. For exam-
ple, Pirk et al. (2016) demonstrated that the degree of convex
curvature in the increasing methane concentration correlated
positively with wind speed (WS) outside the chamber. Fur-
thermore, in the case of soil acting as a methane sink, the
methane consumption by soil methanotrophs obeys the first-
order reaction kinetics, which should lead to curvilinear con-
centration dynamics in the chamber (e.g., Sabrekov et al.,
2016). However, the different processes responsible for the
curvature in the concentration time series may be difficult to
separate from each other (Kutzbach et al., 2007).
There are many studies that have recognized that the use
of linear regression in flux calculation can cause significant
underestimation of the flux (e.g., Healy et al., 1996; Hutchin-
son et al., 2000; Nakano et al., 2004; Livingston et al., 2005,
2006; Kutzbach et al., 2007; Kroon et al., 2008; Pedersen et
al., 2010; Pihlatie et al., 2013). However, many studies have
used linear regression (e.g., Laine et al., 2006; Alm et al.,
2007; Jones et al., 2011; Bergier et al., 2013; Fassbinder et
al., 2013), because under field conditions it is more robust to
random measurement errors than nonlinear methods. More-
over, the use of linear regression is preferred when compar-
ing measurement sites as it is not as sensitive as nonlinear
models to small differences in soil properties (Venterea et
al., 2009). The selection of the optimal fitting method is im-
portant as it can be a large source of uncertainty in flux cal-
culations (Levy et al., 2011; Venterea, 2013).
Although several studies have examined the different fit-
ting methods for calculating fluxes from chamber data, there
exist only a few papers exploring the dynamics of CH4 flux
data that mainly consist of small uptake fluxes and are mea-
sured with automatic chambers coupled to a high-resolution
gas analyzer (e.g., Savage et al., 2014; Ueyama et al., 2015).
In this study, we measured the CH4 flux between a forest
Biogeosciences, 14, 1947–1967, 2017 www.biogeosciences.net/14/1947/2017/
M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1949
Table 1. CN ratio, bulk density, and ash content (±SD) of the peat
at Lettosuo (n= 4).
CN ratio Bulk density (g cm−3) Ash content (%)
Humus 29.2± 1.8 0.005± 0.003 3.1± 0.4
0–10 cm 23.9± 1.0 0.107± 0.014 6.5± 1.5
10–20 cm 24.3± 0.7 0.170± 0.011 3.4± 0.4
floor and the atmosphere continuously throughout 2 years
at a boreal nutrient-rich forestry-drained peatland site with
typically small CH4 exchange rates. We used six automatic
soil chambers and a cavity ring-down spectroscopy analyzer,
which allowed us to measure with a relatively high sampling
rate during each chamber closure and to perform multiple
daily measurements with each chamber. Our particular aims
with this setup were to answer the following questions:
1. What is the optimal fitting method for calculating the
CH4 flux?
2. How large are the diurnal, seasonal, and interannual
variations in the CH4 flux?
3. What is the annual CH4 balance of the study site?
2 Materials and methods
2.1 Site description
The measurements were made in southern Finland at Let-
tosuo (60◦38′ N, 23◦57′ E) (Fig. S1a in the Supplement),
which is a nutrient-rich peatland forest that was drained in
1969 and fertilized with phosphorus and potassium soon
after. The open ditches, located in approximately 45 m in-
tervals (Fig. S1b), were originally about 1 m deep but
have since been partly filled with new vegetation. Before
drainage, the tree stand was dominated by Scots pine (Pinus
sylvestris) with some pubescent birch (Betula pubescens).
After drainage, the stand has developed to a mixture of Scots
pine and pubescent birch in the dominant canopy layer, with
an understorey of Norway spruce (Picea abies) with some
scattered small-sized pubescent birch. The stem volumes at
the time of this study equaled 174, 46, and 28 m3 ha−1 for
Scots pine, pubescent birch, and Norway spruce respectively.
The tree stand is quite dense, which results in irregular shad-
ing and, consequently, patchy and variable ground vegetation
layer. For example, herbs such as Dryopteris carthusiana and
Trientalis europaea and dwarf shrubs such as Vacciniummyr-
tillus are common in the ground vegetation (Bhuiyan et al.,
2017). In addition, the moss layer is patchy and is dominated
by Pleurozium schreberi and Dicranum polysetum with some
Sphagna (Sphagnum girgensohnii, Sphagnum angustifolium,
and Sphagnum russowii) appearing in moist patches.
Table 2. Ground vegetation, all-sided maximum vascular green area
(VGAmax; vascular green surface, m2, divided by forest floor, m2)
and coverage (%) of forest mosses (CFM) and Sphagnum mosses
(CSP).
Chamber Vegetation VGAmax CFM CSP
1 Pleurozium schreberi 2.04 56 0
Dicranum polysetum
Vaccinium myrtillus
2 Pleurozium schreberi 0.85 60 0
Dicranum polysetum
Vaccinium vitis-idaea
3 Maianthemum bifolium 0.01 3 0
Pleurozium schreberi
Dicranum polysetum
4 Dryopteris carthusiana 2.34 26 0
Vaccinium myrtillus
Vaccinium vitis-idaea
Pleurozium schreberi
Dicranum polysetum
5 Pleurozium schreberi 0.11 30 0
Dicranum polysetum
6 Sphagnum girgensohnii – 0 90
CN ratio of the surface peat, sampled at four points located
at a 20–40 m distance from the chamber plots, averaged 24
for the 0–20 cm layer (Table 1). The relatively low CN ratio is
typical for fertile peatland forests and reflects the fen history
of the site. The bulk density of these samples was 0.11 and
0.17 g cm−3 for the 0–10 and 10–20 cm layers, respectively,
while the average bulk density of the 0–20 cm layer below
each chamber varied from 0.03 to 0.13 g cm−3 (Koskinen et
al., 2014). The ash content of the peat varied from 3.4 to
6.5 %.
The vascular green area (VGA) was estimated for each
chamber and vascular plant species every 2 weeks during the
growing seasons 2011 and 2012 (Ojanen, unpublished data).
This was done by estimating the number and dimensions of
leaves within each chamber and calculating green area by
species-specific regression models between leaf dimensions
and green area. For Vaccinium myrtillus, the surface area of
the green stems was also included into VGA. The coverage
of the mosses was estimated visually. The maximum VGA
and the coverages for each chamber are shown in Table 2.
2.2 Flux measurement system and ancillary
measurements
The automatic chamber measurement system is the same as
used for CO2 exchange by Koskinen et al. (2014). The CO2
flux measurements started in autumn 2010, and the CH4 ana-
lyzer was added to the system in March 2011. Here we report
the CH4 fluxes measured from then until April 2013. Forest
floor gas exchange, including the tree roots, was monitored
using six transparent soil chambers connected to an instru-
ment cabin. The cabin was located at a distance of about 30 m
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1950 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
from the 25.5 m tall EC mast (Koskinen et al., 2014) from
which the WS above the canopy was measured. The loca-
tions of the chambers were selected to maximize the number
of different ground vegetation compositions (Table 2) within
a circle of ca. 15 m radius around the cabin.
The details of the chamber system can be found in Kosk-
inen et al. (2014), and thus here we only describe the main
features of the system. The size of the chamber boxes were
57 cm× 57 cm× 30 cm (length×width× height). We used a
permanently installed steel collar (height 5 cm, inserted at a
depth of 2 cm) below each chamber to minimize the distur-
bance to the soil and to enhance the sealing between the soil
and the chamber. There was a U profile at the bottom of the
chamber edges, insulated with a foam tape, to further im-
prove the sealing. In winter, the whole chamber frame was
raised above the snow level by placing one or two extension
collars (height 16 cm) between the frame and soil.
A 24 V fan (Maglev KDE2408PTV1, Sunon Ltd, Kaohsi-
ung, Taiwan) (size 8 cm× 8 cm) was used to mix the air in-
side the chamber headspace. The voltage of the fan was regu-
lated to keep the mixing steady, but as low as possible (Kosk-
inen et al., 2014). Sample gas was drawn from the chamber
typically once an hour (with some exceptions explained be-
low) at a flow rate of about 1 L min−1 and returned back to
the chamber from the gas analyzers. CH4, CO2, and water
vapor concentrations were measured approximately every 4 s
with a Picarro G1130 cavity ring-down spectroscopy gas an-
alyzer (Picarro Inc., Santa Clara, CA, USA). The inlet and
outlet gas tubes (Festo Oy, Vantaa, Finland) were made of
polyurethane and were 15 m in length and had an inner and
outer diameter of 4 and 6 mm respectively.
The tubes were flushed with ambient air just before the
chamber was closed. When all the chambers were open, am-
bient air was sampled. The delay in the analyzer response
caused by the long tubing was taken into account using a
flagging system in the computer program collecting the data,
which labeled each data point with the respective chamber
number using a 20 s lag. However, as the flow rate varied
slightly in time, some points were removed from the data be-
fore the flux calculation (Sect. 2.4).
Air and soil temperature data were collected every 10 s us-
ing Pt100 probes (PT4T, Nokeval Oy, Nokia, Finland) and
Nokeval 680 loggers (Nokeval Oy, Nokia, Finland). One
probe was located inside each chamber at a height of 30 cm
and positioned next to the fan under a metal heat shield to
prevent direct solar radiation from affecting the measure-
ments. Furthermore, soil surface temperature was monitored
inside each chamber just below the surface of the moss or lit-
ter layer. In addition, soil temperature probes were placed
at depths of 2, 5, 10, 20, and 30 cm at one location near
the chambers. Water table level (WTL) was monitored ev-
ery hour at four different points at the site (TruTrack WT-
HR data loggers, Intech Instruments Ltd, Auckland, New
Zealand). The air pressure, precipitation, and snow depth
data were acquired from the nearby Finnish Meteorological
Institute observatory at Jokioinen (∼ 35 km northwest of Let-
tosuo).
2.3 Meteorological conditions
The climate at the site has both continental and maritime
influences. The annual mean temperature and precipitation
at the nearby weather station in 1981–2010 were 4.6 ◦C
and 627 mm respectively (Pirinen et al., 2012). During this
study, the first measurement year (April 2011–March 2012)
was significantly warmer (annual mean temperature 5.8 ◦C)
than the second measurement year (April 2012–March 2013)
(1.4 ◦C) (Fig. 1). The first year was slightly warmer and the
second year was significantly colder than the long-term mean
recorded at the nearby weather station (4.6 ◦C). Both the
summer (JJA) (17.6 ◦C) and winter (DJF) (2.7 ◦C) temper-
atures in 2011 were warmer than those of 2012 (12.1 and
−2.3 ◦C). In particular, the beginning of summer 2012 was
much colder than the same period in 2011.
Annual precipitation during the first (976 mm) and sec-
ond (780 mm) measurement years was higher than the long-
term mean (627 mm). Summertime precipitation was 9 %
higher in the first (309 mm) year as compared to the second
(284 mm) year, while in winter the difference was 18 % (577
and 490 mm in the first and second winters respectively). The
first snow appeared on 5 December in 2011 and 25 October
in 2012, and the first permanent snow was recorded on 7 Jan-
uary in 2012 and 28 November in 2012. In spring (MAM)
2011, the snow had melted by 13 April. For spring 2012,
we do not know the exact day of snowmelt due to missing
data, although the snow had melted at latest by 4 April. From
the temperature data we estimate that the snow cover disap-
peared sometime in mid-March.
WTL varied from −8 to −59 cm from the soil surface
(negative sign denotes WTL below the surface) and was
highest in the spring and late autumn (SON). The lowest (i.e.,
deepest) values were recorded at the end of summer. The av-
erage WTL in summer 2011 was−47.2± 7.4 cm (±SD) and
−49.1± 7.1 in summer 2012. Occasional sudden increases
in WTL were observed after rainfall events and it usually
took 1–2 weeks to reach the WTL observed prior to the event.
2.4 Flux calculation
During the study period, the chambers were operated with
varying closure times ranging from 2 to 16 min. In 2011,
2 min closures were used with the exception of 6 min mea-
surements made four times per day. After mid-March 2012,
the minimum closure time was 6 min. Thus, each chamber
was typically sampled once an hour, with the exception of
summer 2012 (JJA) when a longer closure time of 16 min
was tested and each chamber was sampled every 2 h. For the
analysis of CH4 exchange dynamics (Sect. 3.3–3.4), we used
the fluxes calculated with a 6 min closure time (as justified in
Sect. 3.2). In addition to removing 20 s from the start of the
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M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1951
1 Jun 2011 1 Sep 2011 1 Dec 2011 1 Mar 2012 1 Jun 2012 1 Sep 2012 1 Dec 2012 1 Mar 2013
30
20
10
0
10
20
30
T
e
m
p
e
ra
tu
re
 [
C
]
Air temperature
2 cm soil temperature
0
20
40
60
S
n
o
w
 d
e
p
th
 [
cm
]
1 Jun 2011 1 Sep 2011 1 Dec 2011 1 Mar 2012 1 Jun 2012 1 Sep 2012 1 Dec 2012 1 Mar 2013
60
50
40
30
20
10
0
W
T
L 
[c
m
]
0
20
40
60
P
re
ci
p
it
a
ti
o
n
 [
m
m
]
(a)
(b)
Figure 1. (a) The daily mean of air temperature (red) and soil temperature at 2 cm depth (blue) at Lettosuo during the measurement period
(1 April 2011 to 31 March 2013) and the daily snow depth (bars) measured at the nearby Jokioinen observatory. (b) The daily mean water
table (WTL) (line) and its standard deviation (shading) from four different points at Lettosuo and the daily precipitation (bars) measured at
Jokioinen.
measurement due to lag caused by long tubing (Sect. 2.2),
18 s was discarded from the start of a measurement to ensure
that the air inside the chamber was properly mixed. Dilu-
tion and spectral corrected CH4 concentrations reported by
Picarro G1130 were used to calculate the fluxes.
Two different regression types were fitted to the data:
linear and exponential. The linear function describing the
change in the concentration, C, as a function of time was
C (t)= alin+ blint, (1)
where alin and blin are parameters and t is the time from the
start of the closure. In this model, the slope blin equals the
concentration change in time.
The exponential function we fitted was
C (t)= aexp+ bexp exp(cexpt), (2)
where aexp, bexp, and cexp are parameters. When differentiat-
ing Eq. (2) with respect to time and inspecting the moment
when the chamber closes (t =0), it follows that the concen-
tration change with time is the product of parameters bexp
and cexp. It is generally considered that this initial rate of
concentration change best represents the flux at that time.
However, when fitting the exponential function to the data
using the least-squares approach, the fitting frequently fails
due to local minima. To overcome this and to avoid over-
parameterization, a Taylor power series expansion (Kutzbach
et al., 2007) was fitted to the data to determine initial esti-
mates of the parameters of the exponential regression.
The exponential regression should capture the flux better
than the linear regression as it takes into account the change
in the gradient between soil and chamber headspace during
chamber closure, which is evident when diffusion flux is de-
creasing the concentration difference. However, exponential
regression is very sensitive to possible disturbances to the
data at the beginning of chamber closure. In our study, we at-
tempted to minimize these disturbances by closing the cham-
ber slowly and smoothly, which seemed to prevent pressure
fluctuations related to chamber closing. For the analysis of
CH4 exchange dynamics (Sect. 3.3–3.4), we used flux data
that are based on a combination of linear and exponential fits:
first all fluxes were calculated using the linear regression, and
below and above a limit of 2.5 µg CH4 m−2 h−1 the fluxes
were calculated with the linear and exponential method re-
spectively (for justification see Sect. 3.1).
The CH4 flux (F , µg CH4 m−2 h−1) was calculated ac-
cording to Eq. (3), which is based on the ideal gas law:
F =
(
dC(t)
dt
)
t=0
MPV
RTA
3600
s
h
, (3)
where
(
dC(t)
dt
)
t=0 is the time derivative (ppm s
−1) of a lin-
ear (blin) or exponential (bexp× cexp) regression at the be-
ginning of the closure, M is the molecular mass of CH4
(16.042 g mol−1), P is air pressure (Pa), R is the universal
gas constant (8.31446 J mol−1 K−1), T is the mean cham-
ber headspace temperature during closure (K), and V and
A are the volume (m3) and the base area (m2) of the cham-
ber headspace respectively. Here, a micrometeorological sign
convention is used: a positive flux indicates a flux from the
ecosystem to the atmosphere (emission) and a negative flux
indicates a flux from the atmosphere into the ecosystem (up-
take).
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1952 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
When estimating the volume of the chamber headspace,
the height of the moss and snow surfaces was assumed to rep-
resent the interface between the soil and air. In other words,
the pore space in the soil and snow was ignored from the
headspace volume. The error caused by this in flux calcula-
tions was estimated to be only a few percent (Koskinen et
al., 2014). To create a continuous data set of snow depth, the
manual measurements carried out irregularly at the site were
combined with those measured daily at the Jokioinen obser-
vatory. In addition to snow depth, the height of the chamber
headspace was measured at the start and end of the growing
season from 16 points inside each collar by gently placing the
end of a tape measure on top of the surface mosses (Koskinen
et al., 2014). The height of the chamber headspace between
these manual measurements was determined with linear in-
terpolation.
All the calculations and analyses were made with the
Python programming language (Python Software Founda-
tion, version 2.7, https://www.python.org) using the fol-
lowing libraries: NumPy (http://www.numpy.org/), SciPy
(http://www.scipy.org/), Pandas (http://pandas.pydata.org/),
and matplotlib (http://www.matplotlib.org). All the Python
scripts were developed specifically for this study. For the
fits, the least-squares method was used through the “polyfit”
function of NumPy library for the linear regression and the
“curve_fit” function of SciPy library for the nonlinear fits.
2.5 Filtering of the flux data
After the fluxes were calculated, several filters were applied
to remove cases where the measurement system did not work
adequately. The most common reason for discarding data
was due to the problems with the chamber operation, for
example, for the improper functioning of a linear actuator,
which caused the chambers to remain stuck either open or
closed. These cases were detected by monitoring the simulta-
neously measured CO2 concentration data during the closure.
The goodness of fit was checked by calculating the normal-
ized root mean square error (NRMSE) (e.g., Christiansen et
al., 2011; Pihlatie et al., 2013) for each fit:
NRMSE=
√
1
n
n∑
i=1
(Cfit,i −Ci)2
Cmax−Cmin , (4)
where n is the number of measurement points, Cfit,i is the
CO2 concentration calculated from the fit, Ci is the mea-
sured CO2 concentration, and Cmax and Cmin are the high-
est and lowest concentrations measured during closure. If the
NRMSE was larger than 0.05, the CH4 data from that closure
were discarded. It should be noted that the application of this
criterion removes closures with no change in CO2 concen-
tration, which may result when photosynthesis rate equals
respiration rate. Here we found < 20 of such cases, mean-
ing that this criterion could be applied without removing a
significant amount of potentially suitable data.
Figure 2. Concentration data during one chamber closure for
a case with a higher (a linear and exponential: −90 and
104 µg CH4 m−2 h−1 respectively) and lower (b lin −3.5, exp
−4.3 µg CH4 m−2 h−1) flux.
In addition to NRMSE filtering, the running mean of CH4
flux (FCH4) with a time window of 14 days (shifting one day
at a time) and the corresponding standard deviation (σ) were
calculated to remove random spiking in the data. The data
points that failed to fall within FCH4 ± 10σ were removed it-
eratively. In total, 71229 closures were recorded from which
14 % (n= 9987) were discarded due to large NRMSE values
(problems with the chambers) and < 0.001 % (n= 40) were
removed with the σ filter as outliers.
2.6 Detection limit
The minimum detectable flux (MDF) was estimated by using
the metric originally developed by Christiansen et al. (2015),
which was modified by Nickerson (2016) to make it more
suitable for high-frequency measurements:
Biogeosciences, 14, 1947–1967, 2017 www.biogeosciences.net/14/1947/2017/
M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1953
80 60 40 20 0 20
Flux, linear fit [
gCH4
m2h
]
300
200
100
0
100
200
Fl
u
x
, 
e
x
p
o
n
e
n
ti
a
l 
fi
t 
[
g
C
H
4
m
2
h
]
7 6 5 4 3 2 1 0
10
5
0
5
Figure 3. Bin averages (n= 500) of the linear and exponential fluxes of the whole data set (6 min closures only). In the small zoomed figure
the red vertical line denotes the selected flux limit of 2.5 µg CH4 m−2 h−1. Vertical and horizontal error bars show the standard deviation of
flux determined with the exponential and linear fit respectively.
MDF=
 PI
tc
√
tc
ps
( VP
ART
)
M, (5)
where PI is the analytical precision of the instrument (ppm),
tc is the closure time of the chamber (h), and ps is the sam-
pling periodicity (h). The PI for the Picarro G1130 analyzer,
tested and reported by the manufacturer for the specific in-
strument used in this study, was 0.256 ppb and ps was 5 s. On
a typical summer day (T = 20 ◦C), the MDF of the system
was about 0.06 µg CH4 m−2 h−1. However, during winter the
MDF was higher due to lower temperatures and the use of the
extension collars, which together about double the headspace
volume (without snow) and therefore also the MDF.
2.7 The annual balance and its uncertainty
The annual balance of CH4 was estimated for each chamber
by first calculating the daily flux sums from the hourly fluxes
and then summing these over a year. The gaps in the data
were filled by using linear interpolation between the existing
hourly and daily fluxes. As most of the fluxes in 2011 and in
the first quarter of 2012 were measured with a 2 min closure
time, which was considered too short for the exponential re-
gression (Sect. 3.2), we corrected the fluxes calculated with
linear regression from the 2 min closures to correspond to
those measured using a 6 min closure available four times a
day during this period as a reference. This correction was im-
plemented by calculating the daily median ratios between the
fluxes from 6 and 2 min closure times, which were smoothed
by a running median with a moving window of 14 days. Fi-
nally, the 2 min data from 2011 to March 2012 were multi-
plied by this ratio (Fig. S2).
The uncertainty of the CH4 balance estimate derived from
the measurements was evaluated by identifying three key er-
ror sources: (1) the random error of regression, (2) the error
caused by gap filling, and (3) the error caused by the cor-
rection of the fluxes measured using the 2 min closure time
during the first measurement year. First, because the annual
balance of each chamber was calculated from the mean daily
fluxes, we estimated the daily random error as the squared
sum of the uncertainties of the hourly flux data of each day.
Assuming that the goodness of fit reflects all the uncertainties
related to a single flux measurement, the standard deviation
of the slope estimate obtained
((
dC(t)
dt
)
t=0; Eq. 3
)
provides
a measure of this uncertainty.
Next, the error caused by the gap-filling procedure was es-
timated by removing 1 month of flux data from different parts
of the whole data set and inspecting how this affected the an-
nual balance of the different chambers. The average value of
the effect of these monthly gaps was calculated and down-
scaled to represent the effect of one missing day. Multiply-
ing this value by the number of missing days during the year
gives an estimate of the gap-filling error. It must be noted that
the length of the removed period was similar to the longest
gap observed in our data.
Last, the error estimate related to the ratio used to trans-
form the fluxes calculated from 2 min closure to represent the
6 min closure was estimated from the median absolute devi-
ation assuming normally distributed medians. Finally, these
three error estimates were added together by using the stan-
dard accumulation principle of independent errors.
www.biogeosciences.net/14/1947/2017/ Biogeosciences, 14, 1947–1967, 2017
1954 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
Figure 4. The linear (a) and the exponential flux (b) as a function
of fitting period. The fluxes are scaled by the flux calculated with
the longest fitting period (900 s). The error bars show the 95 % con-
fidence intervals. The data are from summer 2012.
As our measurements started in April 2011 and ended in
March 2013, after exactly 2 years, from now on in this pa-
per the expressions “first year” and “second year” denote
the time periods of April 2011–March 2012 and April 2012–
March 2013 respectively.
3 Results
3.1 Flux calculation method
Examples of typical concentration development inside a
chamber during one measurement are shown in Fig. 2, for
both “high flux” case in summer (Fig. 2a) and a “low flux”
case in winter (Fig. 2b). In summer and autumn, when the
0 100 200 300 400 500
Fit starting point [s]
29
28
27
26
25
24
23
22
21
C
H
4
 f
lu
x
 [
g
C
H
4
m
2
h
]
Linear
Exponential
Flux limit method
Figure 5. Fluxes calculated with the linear, exponential, and “flux
limit” methods using a 6 min fitting period with different starting
points for the fits. The error bars show the 95 % confidence intervals.
The data are from summer 2012.
fluxes were the highest, the concentration development in-
side a chamber usually was not adequately approximated by
a linear function and thus the slope calculated with the lin-
ear regression (Eq. 1) did not properly represent the initial
“undisturbed” slope from which the flux should be calcu-
lated. As a result, linear regression resulted in lower flux es-
timates for these cases than exponential regression (Eq. 2).
However, during the periods when the flux approached the
detection limit and the concentration data became noisier,
the use of exponential regression resulted in noisier flux data.
Often, exponential regression created a sharp slope at the be-
ginning of the fit in the concentration time series that resulted
in unphysically high fluxes. To be able to reliably estimate
the CH4 exchange for the whole range of fluxes, we deter-
mined the flux limit below which the exponential regression
resulted in unreliable flux estimates and the linear fit should
be preferred. This limit was estimated by comparing bin
(n= 500) averages of linear and exponential fluxes for the
whole data set (using a 6 min closure time) (Fig. 3). When the
linearly calculated fluxes fell below ca. 2.5 µg CH4 m−2 h−1,
the noise in the flux calculated using the exponential re-
gression increased steeply and the shape of the relationship
changed (Fig. 3). Therefore, we decided to first calculate the
flux with the linear regression and to recalculate all the fluxes
exceeding the limit of 2.5 µg CH4 m−2 h−1 with the exponen-
tial regression. Henceforth, all the data shown in this paper
have been calculated in this way unless stated otherwise.
The whole 2-year data set showed that the CH4 fluxes cal-
culated with linear regression (Eq. 1) were systematically
and significantly lower than those calculated with exponen-
tial regression (Eq. 2) (Table 3). The seasonal average flux
Biogeosciences, 14, 1947–1967, 2017 www.biogeosciences.net/14/1947/2017/
M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1955
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Fl
u
x
 [
g
C
H
4
m
2
h
]
Chamber 1
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Chamber 2
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Chamber 3
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Fl
u
x
 [
g
C
H
4
m
2
h
]
Chamber 4
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Chamber 5
Ju
n
 2
0
1
1
S
ep
 2
0
1
1
D
ec
 2
0
1
1
M
ar
 2
0
1
2
Ju
n
 2
0
1
2
S
ep
 2
0
1
2
D
ec
 2
0
1
2
M
ar
 2
0
1
3
150
100
50
0
50
100
150
200
Chamber 6
Figure 6. Hourly CH4 fluxes from April 2011 to March 2013 measured in each chamber. Negative values indicate uptake by the soil, and
positive values indicate emission to the atmosphere. Fluxes have been calculated using the exponential fit unless the value of the flux obtained
from the linear fit was below 2.5 µg CH4 m−2 h−1.
difference between the linear and exponential regressions
varied within 10.9–44.4 % (average over 2 year 27.5± 0.3 %,
±95 % confidence interval). The mean relative difference
was dependent on the time of the year: it was largest during
the winter and spring (24.9–44.4 %) when the soil CH4 sink
was at its lowest and smallest in summer and autumn (10.9–
14.4 %) when the sink was at its highest. When compar-
ing individual measurements, the average relative difference
between the linear and exponential regression was slightly
smaller in 2012 compared to 2011. Also, the uncertainties
associated with the fluxes were slightly larger in 2011 due
probably to the fewer measurements available with 6 min clo-
sure time.
3.2 Effect of closure time on fluxes
The effect of the different fitting time windows was tested
by both increasing the fitting period from the beginning of
the closure with 10 s steps and by keeping the fitting win-
dow constant but moving its starting point. For these tests,
we used the data from summer 2012, when the measurements
were made with a 16 min closure time. The flux from the ex-
ponential fit was clearly affected by the length of the fit when
the fitting period was < 190 s (Fig. 4b). After that, the mean
difference was mostly statistically insignificant (p> 0.05),
as compared to the flux calculated with the 900 s period.
However, the estimated linear flux stayed about the same for
the first 140 s resulting in 16.2± 0.6 % higher fluxes than ob-
tained with the 900 s fitting window (Fig. 4a). However, fur-
ther increase of the fitting period systematically decreased
the estimated flux by about 1.3 % per 60 s. A decrease of
17.3± 3.0 % was also observed when the starting point of
the fit was delayed by 530 s, but the fitting period was kept
constant at 6 min (Fig. 5).
Even though the results above might support the selection
of a fitting period of 190 s, a 6 min fitting period was applied
in further analysis. This was selected based on three argu-
ments: (1) it made the exponential regression results more
stable; (2) we wanted to use the same fitting period in both
linear and exponential regressions; and (3) a longer fitting
period decreases the detection limit (Eq. 5). The last point
was mainly related to winter measurements when the detec-
tion limit was increased by lower temperatures and the use
of extension collars (increasing the effective volume before
the collars were filled with snow). However, in 2011 and in
the first quarter of 2012, a 2 min closure time was mostly
used, which proved to be too short for accurate estimates
with the exponential fit. As a result, the results from these
shorter measurements were corrected to correspond to those
obtained with the 6 min closure time (Sect. 2.7).
www.biogeosciences.net/14/1947/2017/ Biogeosciences, 14, 1947–1967, 2017
1956 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
Table
3.Seasonal
(sum
m
er
is
JJA
,autum
n
is
SO
N
,w
inter
is
D
JF,spring
is
M
A
M
)
averages
of
C
H
4
flux
(µg
C
H
4
m −
2
h −
1
)
calculated
w
ith
linear
(“linear
flux”)
and
exponential
regression
(“exponentialflux”)w
ith
95
%
confidence
intervals
(±
).T
he
difference
show
s
how
m
uch
sm
allerthe
linearflux
w
as
on
average
w
hen
com
pared
to
the
exponentialflux.T
he
data
include
the
fluxes
m
easured
by
allsix
cham
bers
w
ith
a
6
m
in
closure
tim
e.
Sum
m
er
Sum
m
er
A
utum
n
A
utum
n
W
inter
W
inter
Spring
Spring
A
pr2011–
2011
2012
2011
2012
2011–2012
2012–2013
2011
2012
M
ar2013
M
ean
linearflux
−
38.9±
1.3
−
28.7±
0.6
−
39.0±
1.2
−
31.3±
0.4
−
18.1±
0.7
−
4.5±
0.1
−
6.8±
0.5
−
9.5±
0.4
−
18.6±
0.2
M
ean
exponentialflux
−
45.1±
1.5
−
32.2±
0.7
−
44.9±
1.3
−
34.9±
0.4
−
21.0±
5.3
−
4.8±
5.2
−
25.9±
26.5
−
12.3±
1.2
−
22.3±
0.4
N
um
berofclosures
1558
3685
1477
10
642
1597
12
209
3180
10
272
48
182
D
ifference
(%
)
14.4±
0.5
11.7±
0.3
14.2±
0.5
10.9±
0.2
24.9±
1.0
38.9±
0.8
44.4±
1.5
38.2±
1.0
27.5±
0.3
Figure 7. The frequency distribution of fluxes measured with all
chambers in (a) different years and (b) different summers. The
fluxes were grouped into classes of 10 µg CH4 m−2 h−1.
3.3 Seasonal dynamics of CH4 flux and comparison
between the chambers
During the 2-year measurement period, CH4 fluxes varied
mainly between−120 and+20 µg CH4 m−2 h−1 (Figs. 6 and
7). Higher uptake rates (70 µg CH4 m−2 h−1) were measured
more often during the first year (Fig. 7a) and during summer
2011 (Fig. 7b) than in the second year and in summer 2012.
The number of emission cases was low in both years and the
soil acted as a CH4 sink for most of the time in all chambers,
although a few emission peaks of up to 200 µg CH4 m−2 h−1
were recorded during and following heavy rainfall events.
The data filtering (Sect. 2.5) was designed to be flexible to
prevent the removal of these short-lasting CH4 bursts from
the accepted data set. While some emission peaks were ob-
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M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1957
Figure 8. (a) Annual CH4 exchange for each chamber for two 1-
year monitoring periods and (b) cumulative CH4 exchange for each
chamber from 1 April 2011 to 31 March 2013. The error bars (a)
and shading (b) include estimations of the random error, the error
caused by gap filling, and the uncertainty of the correction of the
fluxes measured using the 2 min closure time (see Sect. 2.7).
served in most of the chambers, the peaks were largest in
chamber 6. However, the peaks did not necessarily occur at
the same time in different chambers.
CH4 fluxes showed a clear seasonal variation. In spring,
when the snow melted and thawing of the soil surface had
started, CH4 emissions fluctuated around 2 µg CH4 m−2 h−1
in all chambers (Fig. 6). As the temperature rise continued,
increasing CH4 uptake was observed. In both years, CH4
uptake was largest in August, when fluxes varied between
−30 and −130 µg CH4 m−2 h−1. In September, the uptake
decreased and by the end of November it had dropped to half
of that in the summer. However, the soil acted as a sink un-
til the soil surface froze, after which CH4 fluxes fluctuated
around zero.
Considerable systematic differences in fluxes between the
chambers were detected. The largest 2-year average sinks
were measured in chambers 5 and 2 (Fig. 8), which were
dominated by forest mosses Pleurozium schreberi and Di-
cranum polysetum (Table 2). The third largest sink was ob-
served in chamber 6 (Fig. 8) with a Sphagnum sp. carpet,
while the remainder of the chambers showed similar fluxes.
Annual net CH4 exchange rates were on average −267± 55
and −172± 31 mg CH4 m−2 yr−1 (± standard error of the
mean) in 2011–2012 and 2012–2013 respectively. The for-
est floor sink was 10–44 % lower during the second than
first annual period and this difference was statistically sig-
nificant (p < 0.05) for all the chambers except chamber 4.
The largest absolute year-to-year reduction in annual CH4
exchange was observed in the two chambers dominated by
Pleurozium schreberi and Dicranum polysetum (5 and 2),
followed by the chamber dominated by Sphagnum sp. (6).
However, the largest relative decrease in net CH4 exchange
happened in chamber 6 (44 %) while in the rest of the cham-
bers the decrease varied within 10–37 %.
The sink period, i.e., the period when all chambers acted
as CH4 sinks (daily mean flux <−2 µg CH4 m−2 h−1), was
slightly longer in the first than in the second year. In the
first year, all chambers acted as sinks from 14 May 2011 to
20 February 2012, a total of 282 days. During the second
year, the sink period lasted for 269 days from 10 May 2012
until 3 February 2013. In addition, chamber 6 acted as a sink
over the whole winter and spring in 2012, while from cham-
bers 2 and 5 daily mean fluxes of<−2 µg CH4 m−2 h−1 were
measured already at the start of the study in April 2011.
3.4 Factors controlling the short- and long-term
variations in CH4 exchange
3.4.1 Seasonal cycle
There was an observable, exponential relationship between
the mean daily CH4 fluxes and the deeper soil temperatures
when the data from the spring and summer of 2011 were
pooled (Fig. 9a). Splitting these data into shorter periods
showed that the relationship was rather strong in April–May
and in June–early July, but after that, when the soil temper-
ature at 30 cm depth exceeded 12 ◦C, the relationship was
absent. It is evident that there is some covariation between
soil temperature and WTL with typically higher CH4 uptake
taking place at lower WTL. The plot between the residuals
of the temperature response against WTL (Fig. 9b) suggests
that the variation in the CH4 uptake during the latter half of
July and August was better explained by the WTL than tem-
perature. All the chambers recorded similar behavior in 2011
and 2012, although in 2012 the data were noisier and the re-
lationships observed in 2011 were not as clear.
www.biogeosciences.net/14/1947/2017/ Biogeosciences, 14, 1947–1967, 2017
1958 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
Figure 9. (a) Daily CH4 exchange plotted against soil temperature
at 30 cm in chamber 6 for spring (April and May) (triangles), for
the first half of the summer (1 June to 15 July) (circles) and for the
second half of the summer (16 July to 31 August) (crosses) in 2011.
Red curve in (a) denotes the exponential fitting (Eq. 2) to the data.
(b) Residuals of the exponential fitting in (a) against water table
level. (c) Daily CH4 exchange in chamber 6 against water table level
(the same flux data as in panel a).
3.4.2 Diurnal cycle
In addition to seasonal dynamics, diurnal variation was ob-
served in CH4 fluxes at least occasionally in all chambers,
mostly in May and in the first half of June. Such variation
was more common in 2012 and was observed in all of the
chambers, while in 2011 the variation occurred mostly in
chambers 2, 5, and 6. For example, during the first 2 weeks
of June 2011 a clear diurnal cycle coinciding with the vari-
ation in air temperature was observed (Figs. 10 and 11a–b).
Higher CH4 uptake was observed during the night and morn-
ing hours, while the sink decreased towards the midday and
started to grow again towards the night (Fig. 11a). This par-
ticular 2-week period was associated with high daytime air
temperatures, reaching almost +30 ◦C, and a relatively low
WTL (Figs. 10 and 11a–b). After that, at about mid-June, the
weather type changed to cool and wet and the diurnal vari-
ation was diminished or absent (Figs. 10 and 11d–e). Such
behavior, illustrated in Fig. 10, was typical for the rest of the
growing season data: diurnal variation occurred more often
with dry weather, while during and after the rain the varia-
tion ceased for a while. However, WTL itself did not have an
impact on the diurnal cycle.
Pooling the data of these 2-week periods into hourly
means implies that the soil temperature may exert a strong
control on the CH4 exchange (Fig. 11). However, as temper-
ature often – though not always – tends to correlate with wind
speed, particularly in the summer, it is necessary to consider
the effect of both these variables. The correlations calculated
from hourly data indicate that it was the wind speed and not
the temperature which played the major role in causing the
diurnal variation in CH4 flux (Figs. S6–S27). However, this
relationship was not comprehensive, as the correlation with
wind speed was absent during some periods. In qualitative
terms, we observed that the drier the soil was, the greater the
impact of wind speed.
To explain this correlation, we investigated the relation-
ship between the parameter cexp (Eq. 2) and ambient WS in
2-week to 1-month periods to diminish the possible impact of
seasonality (Figs. S28–S40). cexp represents the curvature of
concentration time series during each chamber closure. For
example, the cexp determined for chamber 2 became less neg-
ative when WS exceeded 2 m s−1. This means that the curva-
ture was weaker for cases of high WS.
3.4.3 Correlation between the flux and
meteorological variables
To understand the general driving factors behind all the vari-
ation, either diurnal or seasonal, Pearson correlation coef-
ficients between the hourly CH4 flux and key environmen-
tal variables were calculated for different seasons, averaging
the correlations determined separately for each chamber (Ta-
ble 4).
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M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1959
Jun 6  2011 Jun 9 2011 Jun 12 2011 Jun 15 2011 Jun 18 2011 Jun 21 2011 Jun 24 2011 Jun 27 2011Jun 3, 2011 , , , , , , , ,
Figure 10. Hourly CH4 flux (black circles), air temperature (red curve), and water table level (WTL) (blue curve) in June 2011 in chamber
5. The grey vertical bar shows the split of the data for Fig. 11.
Table 4. Correlation coefficients (r) between hourly CH4 flux and environmental variables averaged for six chambers during different
seasons. All six chambers with p< 0.01 are bolded and underlined; five chambers with p< 0.01 are bolded; four chambers with p< 0.01
are underlined; three chambers with p< 0.01 are italicized. AirT is air temperature, ST is soil surface temperature, PAR is photosynthetically
active radiation, WS is wind speed measured above the canopy, Tx is soil temperature at a depth of x cm, and WTL is water table level. For
clarity, negative r values typically denote situations where CH4 uptake increases when the value of explaining variable increases. The season
definitions are the same as in Table 3.
Season AirT ST PAR WS T2 T5 T10 T20 T30 WTL∗
Spring 2011 −0.03 −0.04 −0.18 −0.08 − 0.41 − 0.52 − 0.61 − 0.67 − 0.70 0.52
Summer 2011 −0.05 0.05 0.17 0.30 0.08 −0.26 −0.37 − 0.54 − 0.61 0.60
Autumn 2011 − 0.19 − 0.16 0.16 0.40 − 0.19 − 0.19 − 0.2 − 0.21 − 0.22 0.39
Winter 2011–2012 − 0.34 −0.23 −0.17 −0.05 − 0.70 − 0.75 −0.59 − 0.83 − 0.83 − 0.83
Spring 2012 − 0.48 − 0.57 0.00 0.15 − 0.69 − 0.74 nd − 0.82 − 0.82 0.47
Summer 2012 −0.16 −0.17 0.14 0.21 − 0.30 − 0.42 nd − 0.60 − 0.65 0.59
Autumn 2012 − 0.47 − 0.53 0.11 0.28 − 0.58 − 0.61 − 0.45 − 0.64 − 0.64 0.60
Winter 2012–2013 0.29 0.37 0.07 0.02 − 0.37 − 0.73 − 0.79 − 0.79 − 0.79 − 0.35
∗ Negative WTL denotes water level below the soil surface, i.e., positive correlation results from increasing uptake with decreasing WTL. nd means not determined
There was a highly significant negative correlation be-
tween CH4 flux and soil temperature (i.e., higher uptake at
higher temperature). The deeper soil temperatures (at 20 and
30 cm depths) showed the best correlation in all seasons.
Also, T5 and T2 often correlated with CH4 flux. The high-
est correlations were observed in springs, winters, and in au-
tumn 2012, and all these correlations were significant in all
the chambers with the exception of summer 2011. Also, the
correlations of ambient and soil surface temperature were
systematically lower than those of the deeper soil tempera-
tures. The correlation with surface soil temperatures was ab-
sent or very low in summer 2011, when only the deeper soil
temperatures showed a significant correlation.
WTL and CH4 flux correlated positively in both summers
(i.e., the deeper the WTL, the higher the uptake), while a
negative correlation (i.e., the deeper the WTL, the higher the
emission) was found for the winters. The correlation between
the flux and PAR was always low (|r|< 0.2) or absent.
A significant positive correlation between WS and the
flux was found in both summers and autumns and in spring
2012, meaning that the estimated sink decreased when WS
increased. This correlation was especially clear in the time
periods when there was diurnal variation in the flux, but it
was nonexistent when no diurnal cycle was observed, which
is consistent with the result reported above. However, even
though the correlation was high in autumn 2011, no statis-
tically significant diurnal variation in the flux was observed
at that time (data not shown). Of all the inspected quantities,
WS was the best explanatory factor of the diurnal cycle of
CH4 flux; this was followed by temperature quantities.
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1960 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
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(a) (b) (c)
(d) (e) (f)
 
Figure 11. Diurnal variation of mean CH4 flux (a, d) and soil surface temperature (◦C) (b, e) measured in chamber 2, and the wind speed (c,
f) measured above the canopy, on 2–14 June 2011 (a, b, c) and 15–27 June 2011 (d, e, f). Shading shows the 95 % confidence intervals.
4 Discussion
4.1 Chamber closure time and flux calculation method
In this study, we found that using the linear regression
method in flux calculations resulted in 20–50 % lower flux
estimates for most of the time, in comparison to fluxes
calculated with an exponential fit. However, in winter and
early spring, i.e., at the time of low absolute CH4 fluxes
(< 2.5 µg CH4 m−2 h−1), linear regression gave more reli-
able results with clearly lower hour-to-hour noise in the
fluxes. The uncertainty associated with exponential regres-
sion with low fluxes was caused by the decreased signal-
to-noise ratio in the concentration data, leading to more or
less arbitrary values of the concentration change estimated at
t = 0. This explains why the difference between the fluxes
estimated by the linear and exponential models was highest
during winter and spring.
The use of exponential regression can be considered es-
pecially justified during summer and autumn when the con-
centration development inside the chamber is strongly non-
linear. During these periods, linear regression gave signif-
icantly lower flux estimates with an average difference of
12.8± 1.8 %. In winter and spring, however, the average sea-
sonal difference was as high as 44 %. Concerning the an-
nual balance, it should be noted that this difference has a
greater influence during summer and autumn when the fluxes
are up to 2 orders of magnitude larger. The mean differ-
ence during the whole measurement period (27.5± 0.3 %) is
in agreement with many previous studies; for example, An-
thony et al. (1995) and Pedersen et al. (2010) reported a 35
and 34 % decrease in flux values, respectively, when using
linear regression instead of exponential regression. Kutzbach
et al. (2007) reported that underestimations for multiple sites
varied mostly within 20–60 %, while Pihlatie et al. (2013)
found an average underestimation of 30 % under labora-
tory conditions at different flux levels. However, the above-
mentioned studies focused on either CH4 and CO2 emissions
or CO2 uptake and did not include measurements related to
a small soil sink of CH4. Since the exponential fit results in
larger uptake estimates, which we consider to better repre-
sent the correct flux at the time of the chamber closure, we
agree with the previous studies that recommend the use of
exponential regression in flux calculation. However, due to
the considerable noise generated for small fluxes, we rec-
ommend that, in future studies employing temporally high-
resolution data, the fluxes should be calculated initially with
both methods to determine the threshold for “low” fluxes. As
this threshold value is dependent on the measurement system
and method, it cannot be generalized.
We found that increasing the fitting period up to 15 min
from the beginning of the concentration time series system-
atically decreased the flux estimated by the linear regression
model, but only after this period exceeded 140 s. In con-
trast, the flux estimated by the exponential regression de-
creased until the fitting window covered 190 s after which
the estimated flux was stabilized. To disentangle whether
these anomalous patterns in the beginning of both curves
were caused by an initial disturbance to the measurement or
they represented a real phenomenon affecting the flux, we
removed 2 min of data from the beginning of concentration
time series. This removed the plateau with large variation
from the linear fit results but did not change the shape shown
for the exponential fit in Fig. 4b (results not shown). This
suggests that the concentration data during the first minute
of measurement are perturbed by chamber closure and that
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M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1961
the linear fit is more sensitive to this than the exponential fit,
when using a short fitting period. However, the exponential
fit seems to overestimate the flux if the fit is limited to a short
time window, but this overestimation is not related to a pos-
sible disturbance in the beginning of the data.
Because the concentration development is nonlinear, it is
not only the length of the fitting period but also the start of
this period, which is important for the flux estimate. The
more data are removed from the beginning, the smaller the
estimated CH4 uptake becomes. Ueyama et al. (2015) no-
ticed that the flux estimates by linear and exponential re-
gressions both decreased with increasing closure time. Their
slopes of linear regression (14± 2 % over 5 min) decreased
faster than those in our study (16.2± 0.2 % over 13 min),
suggesting that their concentration data were more nonlin-
ear. The difference could be partly explained by the fact
that Ueyama et al. (2015) used smaller chambers and mea-
sured higher fluxes, which both result in a faster decrease of
the vertical concentration gradient between the soil and the
chamber headspace.
4.2 CH4 exchange dynamics in a peatland forest
4.2.1 Annual balances
The measurement site (excluding the ditches) was a
small annual CH4 sink (varying from 172± 31 to
267± 55 mg CH4 m−2 yr−1, ± standard error of the mean)
over the 2-year measurement period. While we do not have
measurements prior to drainage, it is possible to roughly esti-
mate the pre-drainage fluxes from measurements conducted
at similar sites. As Lettosuo was originally a herb-rich, tall
sedge birch-pine fen, it can be considered similar to the site
reported by Nykänen et al. (1998). That site has high CH4
emissions of 25 g CH4 m−2 yr−1, so it is obvious that the
drainage of Lettosuo has turned the peat soil from a CH4
source to a small CH4 sink. However, it should be noted that
our calculations of annual and daily CH4 exchange do not in-
clude the emissions from the ditches, which have been found
to be highly variable: from 0 to 600 mg CH4 m−2 day−1 (e.g.,
Minkkinen et al., 1997; Minkkinen and Laine, 2006; Luan
and Wu, 2015). At Lettosuo, where the ditches cover 2–3 %
of the area, we estimated, based on 41 manual chamber flux
measurements from six points made in the latter half of 2011,
that CH4 emissions (per m2 ditch) from the ditches averaged
22 (±38, ±SD) g CH4 m−2 yr−1 (unpublished data). Simple
upscaling suggests that, when ditches are accounted for, Let-
tosuo is a small annual source of CH4 to the atmosphere, al-
though the high uncertainties associated with this calculation
should be noted.
Previous studies of drained peatland forests in Fin-
land have reported uptake rates varying between 10 and
970 mg CH4 m−2 yr−1 (Alm et al., 1999; Minkkinen et al.,
2007; Ojanen et al., 2010; Lohila et al., 2011). The aver-
age annual uptake in boreal upland forests typically varies
from about 100 to 500 mg CH4 m−2 yr−1 (Smith et al., 2000;
Dutaur and Verchot, 2007; Lohila et al., 2016), but also an-
nual net emissions from upland forests have been reported
(e.g., Sundqvist et al., 2015; Lohila et al., 2016). Thus, the
net annual CH4 exchange measured at Lettosuo (excluding
the ditches) was well within the typical range of the average
CH4 sinks reported for boreal upland forests.
4.2.2 Emission peaks
A few larger CH4 emission peaks were observed during and
after heavy rainfall events in summer, but not all chambers
responded to the same rainfall events. The largest number
and magnitude of these short bursts of CH4 were recorded
with the Sphagnum-dominated chamber (6), which was ex-
pected as Sphagnum mosses favor wet spots. These rain-
fall events turned the soil from a sink to a source (up to
200 µg CH4 m−2 h−1 in chamber 6) for a short period ranging
from a few hours to few days. This was possibly due to in-
creased water saturation and decreased air-filled pore space
leading to reduction in oxygen diffusion, which could pro-
mote methanogenic activity and suppress methane oxidation.
Similarly to our results, Nykänen et al. (1995) ob-
served that a drained peatland soil can switch to a CH4
source (up to 200 µg CH4 m−2 h−1) during water saturation
event. However, the emission peaks at Lettosuo were rel-
atively small when compared to upland mineral soil for-
est sites, where emissions of up to 3.7 mg CH4 m−2 h−1
have been observed in wet conditions (e.g., Savage et
al., 1997; Lohila et al., 2016). Similarly, the maximum
hourly uptake in summer at Lettosuo was rather similar to
the fluxes reported for the above-mentioned upland forests
(from −50 to −120 µg CH4 m−2 h−1 at Lettosuo vs. −40 to
−80 µg CH4 m−2 h−1 at upland forests).
4.2.3 Spatial variation
There were relatively large differences in the an-
nual net CH4 exchange rates between the cham-
bers (from −104 mg CH4 m−2 yr−1 in chamber 3 to
−505 mg CH4 m−2 yr−1 in chamber 5), even though all the
chambers were located within a maximum distance of about
15 m from each other. The difference in the soil surface
temperature between the chambers was usually less than 2 K,
which indicates that the soil temperature was not the main
factor determining the observed spatial variation in fluxes.
Since we do not have WTL data for each of the chambers
separately, we cannot quantitatively evaluate its role in the
spatial variation of fluxes. It is unlikely that the variation in
the WTL solely could explain the difference: even though
chambers 4 and 5 were located at the same distance from a
ditch, and probably had the deepest WTL, chamber 5 showed
the highest uptake, while chamber 4 was one of the smallest
sinks. Hence, although WTL is likely to explain part of the
spatial variation in the CH4 fluxes, there are potentially
www.biogeosciences.net/14/1947/2017/ Biogeosciences, 14, 1947–1967, 2017
1962 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
many other factors, such as the vegetation composition and
small-scale soil properties. The smallest sink was observed
in chambers 1, 3, and 4, which were characterized with the
lowest (3) and highest (1, 4) vascular green area (VGAmax)
values. Thus it seems that it was not the amount of ground
vegetation which affected the sink, but a more relevant factor
could have been the coverage of mosses vs. that of vascular
plants within the collar, especially that of the forest mosses
Pleurozium schreberi and Dicranum polysetum, which were
particularly abundant in the highly oxidizing chambers 2
and 5. Due to the small number of chambers, however, the
relationship between the forest floor vegetation and the CH4
exchange may be coincidental and can only be speculated.
4.2.4 Diurnal variation
All the chambers recorded diurnal variation in CH4 flux at
some time during the study period with most of the varia-
tion observed during late spring and early summer. Typically,
CH4 uptake was at its highest during the night and decreased
towards the afternoon. The diurnal variation was more com-
mon and occurred more often in all chambers in 2012, while
in 2011 it occurred mostly in chamber 2. This variation usu-
ally ceased or was at least greatly diminished during and after
rainfall events, but usually it appeared again after a couple of
days. WTL as such, however, did not have an impact on the
diurnal cycle, which suggests that the conditions in the soil
surface were much more important for this phenomenon.
Although the diurnal variation seemingly followed the pat-
terns in the air and soil surface temperatures, it was best
explained by the WS measured above the canopy (below
canopy WS is not available). To further study this relation-
ship, we tested the correlation between the parameter cexp
(Eq. 2) and WS. cexp represents the curvature in the exponen-
tial fit, being negative whenever the concentration increase
during a chamber closure shows a slowing shape. As we only
selected negative, i.e., uptake, fluxes here, it follows that a
more negative cexp indicates a higher curvature in the con-
centration evolution. Should leaking be responsible for the
smaller CH4 uptake during daytime, as the observed rela-
tionship between WS and CH4 exchange implied, it would
be logical to find higher curvatures with higher WS. Such a
relationship was recently found by Pirk et al. (2016) for CH4
emission chamber flux data from pristine peatlands. How-
ever, we did not observe such a relationship in our CH4 up-
take data. For example, in chamber 2, in which the diurnal
cycle was most explicit, an increasing cexp was determined
for most of the periods studied. There were only a few cham-
bers and periods when cexp decreased with increasing WS.
Thus we must conclude that the diurnal variation in our data
is related to the technical operation of the chamber rather
than environmental conditions. Nevertheless, as the temper-
ature and WS correlated strongly, it is possible that some of
the observed pattern was due to some microbial or environ-
mental factor.
We hypothesize that, rather than chamber leaking, the
main underlying factor for the clear negative correlation be-
tween WS and CH4 uptake is related to changes in the soil
storage and thus the changes imposed by chamber closure to
the concentration gradient within the top soil and the adja-
cent air layer. Prior to the closure, this gradient is controlled
by atmospheric mixing and hence strongly affected by the
ambient WS. During a calm night with a cool soil surface,
turbulent mixing is strongly suppressed and molecular diffu-
sion gains importance, while windy and sunny conditions re-
sult in much smaller vertical gradients due to vigorous turbu-
lence that is also able to perturb the top-soil pore space. Af-
ter the chamber is closed, the concentration gradient adjusts
to the constant mixing generated by a fan. Thus, the change
in concentration gradient depends on the mixing conditions
that prevail above the target surface just before the chamber
is introduced and how these relate to the mixing rate of the
chamber headspace air. In the nocturnal case outlined above,
mixing is enhanced after the chamber closure, resulting in a
higher CH4 uptake in the chamber.
The absence of the diurnal cycle in winter, and during
and after the rain in summer, can be explained by the in-
creased soil moisture content, which decreases the air-filled
pore space in soil, thus hampering the wind-induced mixing
effect at the soil–atmosphere interface and by slowing down
the diffusion rate (Pirk et al., 2016).
It should be noted that the situation is different when CH4
exchange is measured above a forest canopy with the EC
method. In that case, the measurement does not significantly
disturb atmospheric mixing and increased mechanical turbu-
lence potentially enhances vertical gas exchange. Such pos-
itive correlation between the downward CH4 flux and WS,
with higher sinks during the daytime, has been reported by
Wang et al. (2013). This is consistent with the results of our
fan-speed test, described in Koskinen et al. (2014) who mea-
sured CO2 respiration by the same chamber system. The CH4
flux data from the same test showed a higher CH4 uptake
with higher fan speed (data not shown).
A wind-induced diurnal cycle suggests that the current
chamber setup potentially leads to an over- or underesti-
mate of the actual uptake rate during lower or higher fan-
induced mixing, respectively, as compared to ambient mix-
ing by wind. The chamber construction could be improved by
making the fan speed vary as a function of the ambient wind
speed, so as to mimic the variations in atmospheric mixing.
However, we can expect that the systematic bias resulting
from the wind response is minimized when employing au-
tomated sampling that facilitates continuous measurements.
Our results imply that sporadic sampling with manual cham-
bers, which is typically limited to the daytime, would have
resulted in lower uptake estimates for this site than the ex-
tensive data collected with our automatic system.
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M. Korkiakoski et al.: Methane exchange at the peatland forest floor 1963
4.3 Driving factors for the CH4 efflux
The seasonal CH4 fluxes correlated best with soil temper-
atures at the depths of 20 cm and 30 cm, but significant
correlations occurred also with soil temperatures at other
depths for most of the study period. The correlations with
air and soil surface temperatures were lower. The correla-
tions were always negative, indicating that higher tempera-
tures promoted the soil CH4 uptake. This observation could
be attributed to increased consumption of CH4 by methan-
otrophs in higher temperatures that enhance methanotrophic
activity (e.g., Mohanty et al., 2007). However, it is likely that
in addition to – or even instead of – the increased methan-
otrophic activity, there are other reasons behind this rela-
tionship. The covariation of temperature with other variables,
such as ground water level and phenology, all typically peak-
ing in July–August, may lead to spurious correlation between
temperature and CH4 flux. Indeed, the flux was also corre-
lated with WTL, the correlation being significantly positive
(higher uptake with lower WTL) in spring, summer, and au-
tumn, but negative in winter. At our site, the soil layers most
favorable for methane production and oxidation are located
at clearly different depths in the soil, the first being found
below the water table and the latter much closer to the soil
surface (A. Putkinen, unpublished data). Both of these have
distinct temperature and moisture responses, which are prac-
tically impossible to disentangle by examining the net CH4
flux observed at the surface.
In addition to the correlations found in the hourly data, we
found evidence that lowering WTL increases the daily CH4
uptake in the latter part of summer, when WTL<−40 cm.
In the beginning of the summer, the daily fluxes were better
explained by the soil temperature, while after mid-July the
WTL overshadowed the temperature as a control of the daily
fluxes.
In pristine peatlands, temperature has been shown to cor-
relate positively with the CH4 emission rate (e.g., Mikkelä et
al., 1995; Bellisario et al., 1999; Mastepanov et al., 2013).
In drained peatland forests, significant correlations between
CH4 flux and temperature have been found in CH4-emitting
ecosystems (Nykänen et al., 1998; Minkkinen and Laine,
2006), although the direction of the correlation has been
found to differ between fens and bogs. In contrast, no signif-
icant correlations with temperature were found in peatland
forests that mainly showed CH4 uptake (Ojanen et al., 2010;
Wang et al., 2013). Both CH4 emission and uptake have been
found to correlate with WTL (e.g., Bellisario et al., 1999;
Ojanen et al., 2010).
In addition to temperature, WTL, and WS, CH4 flux has
been found to correlate with tree stand volume (Ojanen et
al., 2010; Minkkinen et al., 2007), which is, in contrast, an
indirect measure of the WTL. Also, PAR has been observed
to correlate positively with CH4 emissions in a Sphagnum-
dominated mixed mire (Mikkelä et al., 1995). In this study,
however, the correlations with PAR were low or absent.
5 Conclusions
In this paper, we have presented a 2-year data set of CH4
exchange measured at the forest floor of a boreal forestry-
drained fen. These results show that automated chamber
measurements with an accurate online gas analyzer make it
possible to observe small CH4 fluxes even during the winter
with snow cover. Although the fluxes at our site were rela-
tively low throughout the year, we succeeded in catching the
annual cycle in the CH4 uptake. Our results indicate that the
forest floor of this peatland site acted as a small annual CH4
sink (mean balance−219 mg CH4 m−2 yr−1), although com-
pleting the balance with the emissions from ditches indicates
that the site is likely to be a small CH4 source.
In spite of the low flux detection limit of the measurement
system, our results indicate that it is necessary to pay atten-
tion to the flux calculation methods, and instead of choosing
between linear and exponential fits we decided on a combi-
nation of both. Even though the fit based on linear regression
was observed to typically result in a smaller flux than an ex-
ponential fit, its use was justified for low fluxes by showing
that it produced more robust estimates when the concentra-
tion change during chamber closure was small and thus more
affected by measurement noise. In addition, we demonstrated
that both the length of the fitting period and the starting time
of this window had a significant effect on the flux estimates
and thus cannot be selected arbitrarily.
The CH4 uptake, measured with closed chambers, was ob-
served to correlate with wind speed, which caused a corre-
sponding diurnal cycle. However, this was partly attributed
to aerodynamic effects due to chamber closure, which are
dependent on atmospheric mixing prior to the closure. Thus,
the chamber construction could be potentially improved by
adjusting the chamber fan speed according to the ambient
wind speed. As this variation is partly related to changes in
the soil CH4 storage, the error introduced in the annual bal-
ance estimated from short-term fluxes can be diminished by
continuous measurements fully covering the diurnal cycle.
Continuous long-term measurements also facilitate the anal-
ysis of the environmental factors that control CH4 exchange.
However, in order to understand the biological processes in-
volved in CH4 production and oxidation, i.e., the processes
behind the net CH4 flux observed, additional measurements
are necessary, focusing on the production and oxidation po-
tentials and the within-soil gas gradients.
Since the considerations of the measurement system per-
formance are site and system specific, we recommend that
any future study should address the procedures involved in
flux calculation, including the fitting method and the length
and delay of the fitting period, based on the analysis pre-
sented above. In particular, we recommend using the flux
limit method applied in this study, i.e., using linear regression
for low fluxes and exponential regression for fluxes above a
threshold to be determined.
www.biogeosciences.net/14/1947/2017/ Biogeosciences, 14, 1947–1967, 2017
1964 M. Korkiakoski et al.: Methane exchange at the peatland forest floor
Data availability. The calculated fluxes and measured headspace
temperatures are included in the Supplement. The rest of the mete-
orological data can be requested from the corresponding author.
The Supplement related to this article is available online
at doi:10.5194/bg-14-1947-2017-supplement.
Competing interests. The authors declare that they have no conflict
of interest.
Acknowledgements. We are grateful for the financial support from
the Maj and Tor Nessling foundation and from the Ministry of
Transport and Communications through the Integrated Carbon
Observing System (ICOS) research. We would also like to thank
Pentti Arffman and Tero Hirvonen for their help in data treatment
and for measurements at the site.
Edited by: U. Seibt
Reviewed by: C.-M. Görres and M. Mastepanov
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