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  <front>
    <journal-meta><journal-id journal-id-type="publisher">BG</journal-id><journal-title-group>
    <journal-title>Biogeosciences</journal-title>
    <abbrev-journal-title abbrev-type="publisher">BG</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Biogeosciences</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">1726-4189</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/bg-14-5189-2017</article-id><title-group><article-title>Year-round CH<inline-formula><mml:math id="M1" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M2" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux dynamics in two contrasting freshwater
ecosystems of the subarctic</article-title>
      </title-group><?xmltex \runningtitle{Year-round CH${}_{{4}}$ and CO${}_{{2}}$ flux dynamics}?><?xmltex \runningauthor{M. Jammet et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Jammet</surname><given-names>Mathilde</given-names></name>
          <email>mathilde.jammet@ign.ku.dk</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Dengel</surname><given-names>Sigrid</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Kettner</surname><given-names>Ernesto</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Parmentier</surname><given-names>Frans-Jan W.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-2952-7706</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Wik</surname><given-names>Martin</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Crill</surname><given-names>Patrick</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-1110-3059</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Friborg</surname><given-names>Thomas</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-5633-6097</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>Center for Permafrost (CENPERM), Department for Geosciences and
Natural Resource Management, <?xmltex \hack{\newline}?> University of Copenhagen,
Copenhagen, 1350, Denmark</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Climate and Ecosystem Sciences Division,
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Department of Arctic and Marine Biology, UiT – The Arctic
University of Norway, Postboks 6050 Langnes, <?xmltex \hack{\newline}?> 9037 Tromsø,
Norway</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Department of Geological Sciences, Stockholm University,
Stockholm, 106 91, Sweden</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Mathilde Jammet (mathilde.jammet@ign.ku.dk)</corresp></author-notes><pub-date><day>21</day><month>November</month><year>2017</year></pub-date>
      
      <volume>14</volume>
      <issue>22</issue>
      <fpage>5189</fpage><lpage>5216</lpage>
      <history>
        <date date-type="received"><day>28</day><month>October</month><year>2016</year></date>
           <date date-type="rev-request"><day>27</day><month>January</month><year>2017</year></date>
           <date date-type="rev-recd"><day>15</day><month>September</month><year>2017</year></date>
           <date date-type="accepted"><day>29</day><month>September</month><year>2017</year></date>
      </history>
      <permissions>
        
        
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/3.0/">https://creativecommons.org/licenses/by/3.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017.html">This article is available from https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017.html</self-uri><self-uri xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017.pdf</self-uri>
      <abstract>
    <p id="d1e175">Lakes and wetlands, common ecosystems of the high northern
latitudes, exchange large amounts of the climate-forcing gases methane
(CH<inline-formula><mml:math id="M3" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>) and carbon dioxide (CO<inline-formula><mml:math id="M4" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) with the atmosphere. The magnitudes
of these fluxes and the processes driving them are still uncertain,
particularly for subarctic and Arctic lakes where direct measurements of
CH<inline-formula><mml:math id="M5" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M6" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions are often of low temporal resolution and are
rarely sustained throughout the entire year.</p>
    <p id="d1e214">Using the eddy covariance method, we measured surface–atmosphere exchange of
CH<inline-formula><mml:math id="M7" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M8" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> during 2.5 years in a thawed fen and a shallow lake of
a subarctic peatland complex. Gas exchange at the fen exhibited the expected
seasonality of a subarctic wetland with maximum CH<inline-formula><mml:math id="M9" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions and
CO<inline-formula><mml:math id="M10" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake in summer, as well as low but continuous emissions of
CH<inline-formula><mml:math id="M11" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M12" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> throughout the snow-covered winter. The seasonality of
lake fluxes differed, with maximum CO<inline-formula><mml:math id="M13" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M14" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux rates recorded
at spring thaw. During the ice-free seasons, we could identify surface
CH<inline-formula><mml:math id="M15" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions as mostly ebullition events with a seasonal trend in the
magnitude of the release, while a net CO<inline-formula><mml:math id="M16" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux indicated photosynthetic
activity. We found correlations between surface CH<inline-formula><mml:math id="M17" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions and
surface sediment temperature, as well as between diel CO<inline-formula><mml:math id="M18" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake and
diel solar input. During spring, the breakdown of thermal stratification
following ice thaw triggered the degassing of both CH<inline-formula><mml:math id="M19" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M20" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>.
This spring burst was observed in 2 consecutive years for both gases, with a
large inter-annual variability in the magnitude of the CH<inline-formula><mml:math id="M21" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> degassing.</p>
    <p id="d1e354">On the annual scale, spring emissions converted the lake from a small
CO<inline-formula><mml:math id="M22" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sink to a CO<inline-formula><mml:math id="M23" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> source: 80 % of total annual carbon emissions
from the lake were emitted as CO<inline-formula><mml:math id="M24" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>. The annual total carbon exchange per
unit area was highest at the fen, which was an annual sink of carbon with
respect to the atmosphere. Continuous respiration during the winter partly
counteracted the fen summer sink by accounting for, as both CH<inline-formula><mml:math id="M25" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M26" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, 33 % of annual carbon exchange. Our study shows (1) the
importance of overturn periods (spring or fall) for the annual CH<inline-formula><mml:math id="M27" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M28" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions of northern lakes, (2) the significance of lakes as
atmospheric carbon sources in subarctic landscapes while fens can be a strong
carbon sink, and (3) the potential for ecosystem-scale eddy covariance
measurements to improve the understanding of short-term processes driving
lake–atmosphere exchange of CH<inline-formula><mml:math id="M29" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M30" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p id="d1e446">Lakes and wetlands are linked to the atmospheric carbon pool via the exchange
of methane (CH<inline-formula><mml:math id="M31" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>) and carbon dioxide (CO<inline-formula><mml:math id="M32" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>), which are two important
climate-forcing gases (Myhre et al., 2013). While wetlands have been a focus
of study due to their high CH<inline-formula><mml:math id="M33" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> source function (Christensen et al.,
2003; Crill et al., 1988; Olefeldt et al., 2013) and carbon sequestration
capacity (Kayranli et al., 2009; Whiting and Chanton, 2001), lakes have only
recently been incorporated together with streams as a separate source into
global CH<inline-formula><mml:math id="M34" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> budgets with an uncertain global emission rate of
8–73 Tg CH<inline-formula><mml:math id="M35" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> yr<inline-formula><mml:math id="M36" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Kirschke et al., 2013). The low number of
experimental studies and the variability in the magnitude of emissions across
lake types (Wik et al., 2016) explain some of this large uncertainty. Carbon
emissions from lakes outweigh part of the land carbon sink, because they emit
CH<inline-formula><mml:math id="M37" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> (Bastviken et al., 2011) and because they respire as CO<inline-formula><mml:math id="M38" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> a portion
of the carbon that is transported laterally from terrestrial soils to lakes
(Algesten et al., 2004; Battin et al., 2009; Cole et al., 2007; Tranvik et
al., 2009). Hence, lakes play an important role within the terrestrial carbon
budget.</p>
      <p id="d1e525">Wetlands and lakes are particularly abundant in the subarctic and boreal
regions (Smith et al., 2007; Verpoorter et al., 2014), where climate warming
is occurring at a faster pace than in the rest of the world (Serreze and
Barry, 2011). In this context, freshwaters have received increasing attention
over the past decade, due to the potential for lakes and particularly Arctic
thermokarst lakes to exert a feedback on climate warming through large
CH<inline-formula><mml:math id="M39" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions (Walter Anthony et al., 2016; Walter et al., 2006). While
non-thermokarst, post-glacial lakes emit less CH<inline-formula><mml:math id="M40" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> per unit area
(Sepulveda-Jauregui et al., 2015; Wik et al., 2016), they cover a larger area
and may as a whole emit half of the total CH<inline-formula><mml:math id="M41" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions
(16.5 <inline-formula><mml:math id="M42" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 9.2 Tg CH<inline-formula><mml:math id="M43" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> yr<inline-formula><mml:math id="M44" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) recently attributed to northern
(&gt; 50<inline-formula><mml:math id="M45" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N) lakes and ponds (Wik et al., 2016).</p>
      <p id="d1e593">Biogenic CH<inline-formula><mml:math id="M46" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> production (methanogenesis) occurs in anoxic environments
such as lake sediments and water-saturated peat (Cicerone and Oremland,
1988). The process is controlled by the interplay between temperature and the
input of organic matter (Kelly and Chynoweth, 1981; Yvon-Durocher et al.,
2014; Zeikus and Winfrey, 1976). In lakes and waterlogged wetlands, CH<inline-formula><mml:math id="M47" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
reaches the atmosphere from its production zone via direct bubble release up
to the surface (ebullition), through emergent vascular plants, or via
turbulence-driven diffusion through the water column (Bastviken et al., 2004;
Lai, 2009; Rudd and Hamilton, 1978). The net flux of CH<inline-formula><mml:math id="M48" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> at the lake
surface is a balance between the production in the sediments and the
oxidation of CH<inline-formula><mml:math id="M49" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> into CO<inline-formula><mml:math id="M50" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> at oxic–anoxic boundaries within the
water column (Casper, 1992). In shallow lakes, ebullition is a main pathway
for CH<inline-formula><mml:math id="M51" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> to reach the atmosphere while bypassing the oxidation zones
(Bastviken et al., 2004). In wetlands, transport from the peat soil to the
surface through vascular plants by passive diffusion or by pressurization
effects depending on the plant species (Brix et al., 1992) is an efficient
pathway for CH<inline-formula><mml:math id="M52" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> to avoid oxidation in the soil and water before reaching
the atmosphere (Joabsson and Christensen, 2001).</p>
      <p id="d1e660">Dissolved CO<inline-formula><mml:math id="M53" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in lakes is produced throughout the water column and
sediments (Casper et al., 2000) or is directly imported from the catchment
(Maberly et al., 2013; Weyhenmeyer et al., 2015). In situ production comes
from the mineralization or the photochemical oxidation of carbon (C) input
from the surrounding catchment (Cory et al., 2014; Dillon and Molot, 1997;
Duarte and Prairie, 2005) and from the degradation of locally produced
organic carbon. CO<inline-formula><mml:math id="M54" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange across the air–water interface is
primarily via diffusive release rather than ebullition (e.g., Casper et al.,
2000). Lake waters are generally observed to be supersaturated in CO<inline-formula><mml:math id="M55" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
with respect to atmospheric values due to in-lake respiration processes
outweighing rates of primary production (Duarte and Prairie, 2005; Sobek et
al., 2005). Hence they are generally CO<inline-formula><mml:math id="M56" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sources to the atmosphere,
albeit nutrient-rich lakes and ponds can be small CO<inline-formula><mml:math id="M57" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sinks during
summer months (Huotari et al., 2011) or an entire summer season (Laurion et
al., 2010; Pacheco et al., 2013; Shao et al., 2015; Striegl and
Michmerhuizen, 1998; Tank et al., 2009).</p>
      <p id="d1e709">Near-surface atmospheric forcing is a key driver for the transport and net
emissions of gases from a lake to the atmosphere. Ebullition of CH<inline-formula><mml:math id="M58" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> in
lakes is partly triggered by water level changes or drops in atmospheric
pressure (Casper et al., 2000; Mattson and Likens, 1990), as a decrease in
the hydrostatic pressure of the overlying water column on gas saturated
sediments favors the release of bubbles (Varadharajan and Hemond, 2012).
Wind-driven turbulence is a recognized driver of diffusion-limited exchange
of CO<inline-formula><mml:math id="M59" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M60" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> across the lake-water interface (Sebacher et al.,
1983; Wanninkhof et al., 1985). Convective mixing due to the cooling of the
lake surface or following the breakdown of thermal stratification in the
water column can increase advection of gas-rich water from the lake bottom,
thus enhancing the diffusion-limited release of gases to the atmosphere
(Eugster, 2003; MacIntyre et al., 2010; Podgrajsek et al., 2015), especially
if the main source of those gases is the sediments, as is the case for
CH<inline-formula><mml:math id="M61" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>.</p>
      <p id="d1e748">Northern ecosystems have strong seasonal contrasts, with short growing
seasons and long snow-covered winters. A snow cover insulates the soil from
very cold air temperatures (Bubier et al., 2002), while an ice lid on a lake
temporarily inhibits the exchanges of gas and heat between the water and the
atmosphere (e.g., Greenbank, 1945) and greatly dampens wind-driven turbulence
in the water column. In lakes, gases can accumulate at the bottom during long
stratification periods, or under lake ice. Lake overturn events most often
occur in spring for seasonally ice-covered lakes and/or in fall if lakes
thermally stratify during summer (Kirillin et al., 2012; Wetzel, 2001).
Overturn events can thus lead to the fast release of accumulated gas to the
atmosphere (Jammet et al., 2015; Michmerhuizen et al., 1996; Phelps et al.,
1998), but also to the input of atmospheric oxygen, thus increasing the
potential for methanotrophy (Kankaala et al., 2006; Schubert et al., 2012).
Extension of observations across all seasons of the year is rare at high
northern latitudes, particularly for lakes, yet is indispensable for reducing
the uncertainty in the magnitude of annual carbon exchange and improving
understanding of the processes driving them.</p>
      <p id="d1e751">Common methods to measure lake–atmosphere fluxes include floating chambers
(e.g., Bastviken et al., 2004), gas transfer models (e.g., Cole and Caraco,
1998),
and bubble traps (e.g., Walter et al., 2008; Wik et al., 2013;
Sepulveda-Jauregui et al., 2015). If these methods are not integrated and
combined, they inherently omit part of the total surface flux. The
application of the eddy covariance (EC) method (Aubinet et al., 2012;
Moncrieff et al., 1997) to lake environments (e.g., Anderson et al., 1999;
Eugster, 2003; Huotari et al., 2011; Mammarella et al., 2015; Podgrajsek et
al., 2014; Shao et al., 2015) offers long-term flux monitoring and is a
potential methodological solution for solving the spatial and temporal issues
of measuring total gas exchange in lakes. Few studies, so far, have used eddy
covariance to quantify long-term CO<inline-formula><mml:math id="M62" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions from boreal lakes
(Huttunen et al., 2011) as well as CH<inline-formula><mml:math id="M63" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from boreal (Podgrajsek
et al., 2014) or subarctic lakes (Jammet et al., 2015). We report here one of
the first year-round eddy covariance measurements of both CH<inline-formula><mml:math id="M64" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M65" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from a seasonally ice-covered lake.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p id="d1e792">Location of the study site <bold>(a)</bold> and flux footprint of the
flux tower in summer averaged over all years <bold>(b)</bold>. The color scale
indicates the extent of the fractional contribution from the source area to
the fluxes measured at the tower. The location of the flux tower is indicated
along with the location of the main environmental data sources.</p></caption>
        <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f01.png"/>

      </fig>

      <p id="d1e807">Surface fluxes were monitored using the eddy covariance method in a subarctic
permafrost peatland undergoing thaw, a landscape with a high percentage of
pond and lake coverage. The location of the flux tower allowed for
measurements to alternate between surface fluxes from a shallow lake and from
a permafrost-free, waterlogged fen-type wetland. The overall aim of this work
was to quantify year-round carbon fluxes in a post-glacial lake, a type
widely present around the subarctic, as compared to the adjacent fen.
Specifically, the objectives were (1) to compare the seasonality of CH<inline-formula><mml:math id="M66" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
and CO<inline-formula><mml:math id="M67" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from two contrasting subarctic ecosystems (lake and fen),
(2) to explore the possibility of identifying short-term environmental
controls on the surface–atmosphere exchange of CH<inline-formula><mml:math id="M68" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M69" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in a
lake, using high, sub-daily temporal resolution measurements covering all
seasons of the year, and (3) to assess and compare the annual atmospheric
carbon budget of a lake and a wetland.</p>
</sec>
<sec id="Ch1.S2">
  <title>Materials and methods</title>
<sec id="Ch1.S2.SS1">
  <title>Study site</title>
      <p id="d1e857">Stordalen Mire is a subarctic peatland complex (68<inline-formula><mml:math id="M70" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>20<inline-formula><mml:math id="M71" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> N,
19<inline-formula><mml:math id="M72" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>03<inline-formula><mml:math id="M73" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> E) with a high lake and pond coverage, located near Abisko
in northern Sweden. Mean annual temperature in the Abisko region has been
increasing and fluctuating around 0 <inline-formula><mml:math id="M74" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C since the 1990s as part of an
accelerated warming trend (Callaghan et al., 2010). Permafrost, which is
discontinuously present in the local mires, has been thawing at an increased
rate since the 1990s in the peatlands of the region, sometimes disappearing
completely (Åkerman and Johansson, 2008). In Stordalen Mire permafrost
thawing has led to changes in microtopography, which controls local
hydrology, which in turn leads to vegetation shifts (Christensen, 2004;
Malmer et al., 2005). This accentuates the heterogeneity of a landscape
comprised of elevated palsas with permafrost, thawing lawns with thermokarst
ponds, and permafrost-free, water-saturated fens. The mire is bordered by
post-glacial lakes on its western, northern, and eastern edges. This study
focuses on the lake Villasjön (Fig. 1) and the adjacent fen to the west
of the tower. According to Olefeldt and Roulet (2012), the two ecosystems are
hydrologically connected with a directional flow from the lake to the fen.</p>
      <p id="d1e905">The wetter fen areas have expanded as a result of permafrost thaw over the
past decades (Johansson et al., 2006). The water table of the fen is at or
above the surface throughout the year. The dominant vegetation species are
vascular plants <italic>Carex rostrata</italic> and <italic>Eriophorium angustifolium</italic>. Villasjön is the largest (0.17 km<inline-formula><mml:math id="M75" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>) lake of the
15 km<inline-formula><mml:math id="M76" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> wide Stordalen catchment containing 27 lakes (Lundin et al.,
2013). It has mean and maximum depths of 0.7 and 1.3 m, respectively
(Jackowicz-Korczyński et al., 2010; Wik et al., 2013). The upstream
catchment of Villasjön is dominated by birch forest (Olefeldt and Roulet,
2012), while its western shore is bordered by thawing palsas. During
snowmelt, there is a small surface inflow feeding Villasjön in the east
(Wik et al., 2013). The lake usually freezes to the bottom in winter. The DOC
concentration in the lake water was measured to be 8.1 mg L<inline-formula><mml:math id="M77" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in 2008
(Olefeldt and Roulet, 2012). Aquatic vegetation is present in the lake, on
its bottom as algae, as submerged plants within its southern arm, and in a
low density of emergent macrophytes at its shores.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Eddy covariance measurements</title>
<sec id="Ch1.S2.SS2.SSS1">
  <title>Measurement setup</title>
      <p id="d1e955">Between June 2012 and December 2014, the surface–atmosphere exchange of
CH<inline-formula><mml:math id="M78" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, CO<inline-formula><mml:math id="M79" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, and latent heat and sensible heat was monitored nearly
continuously with an eddy covariance setup located at the shore of
Villasjön (Fig. 1). Data were logged on a CR1000 (Campbell Scientific,
Inc., UT, USA) until May 2013; from June 2013 it was replaced with a CR3000
(Campbell Scientific, Inc., UT, USA). The 2.92 m high mast was equipped with
a 3-D sonic anemometer (R3-50, Gill Instruments Ltd.) sampling wind
components and sonic temperature at 10 Hz. Throughout the study period,
ambient molar densities of CO<inline-formula><mml:math id="M80" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and H<inline-formula><mml:math id="M81" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O were sampled at 10 Hz with
an open path infrared gas analyzer (IRGA), model LI7500 (LICOR Environment,
NE, USA), mounted on the mast at 2.50 m height. Following lightning that hit
the electric grid in Stordalen Mire on 27 July 2013, the initial LI7500
ceased functioning and was replaced on 1 October 2013 by a different
instrument of the same model.</p>
      <p id="d1e994">From June 2012 to May 2013, the ambient CH<inline-formula><mml:math id="M82" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> mole fraction was sampled at
10 Hz with a closed path Fast Greenhouse Gas Analyzer (FGGA, Los Gatos
Research, CA, USA) in air that was taken from a gas inlet located at 2.50 m
height on the mast through a 6 mm inner diameter polyethylene (PE) tube
using a dry scroll pump (Varian TriScroll 300). The efficient flow rate in
the 95 m long sampling line was 16 L min<inline-formula><mml:math id="M83" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, ensuring the maintenance
of turbulent conditions (Reynolds number ca. 4025). On 5 June 2013, the tube
was replaced with an 8 mm inner diameter PE tube, which changed the flow
rate in the sampling line to 23.88 L min<inline-formula><mml:math id="M84" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Reynolds number ca. 4099).
On 4 August 2013, the closed path CH<inline-formula><mml:math id="M85" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> system was renewed: the IRGA was
changed to a FGGA model 911-010 (Los Gatos Research, CA, USA). Due to
instrumental maintenance, the IRGA was offline between February and
March 2014 and replaced on 24 March 2014 by the previous FGGA. From
August 2013 to December 2014, due to a failure in the electronic connection
between the gas analyzer and the data logger, the raw CH<inline-formula><mml:math id="M86" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> data measured
by the FGGA were pre-processed in order to align the time stamp and frequency
of the gas analyzer recordings with the time stamp of the logger sampling the
wind data. The synchronization procedure was quality-checked after flux
computation (Supplement S2). Each change in the CH<inline-formula><mml:math id="M87" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> measurement setup
was taken into account in the flux calculation.</p>
</sec>
<sec id="Ch1.S2.SS2.SSS2">
  <title>Flux calculation and quality check</title>
      <p id="d1e1064">CO<inline-formula><mml:math id="M88" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, CH<inline-formula><mml:math id="M89" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, sensible and latent heat fluxes, as well as atmospheric
turbulence quantities were calculated and output as 30 min averages using
the EddyPro version 5.2 open-source software (hosted by LICOR Environment,
USA). Processing of the 10 Hz raw data followed standard eddy covariance
procedures (Aubinet et al., 2012; Lee et al., 2005); methodological choices
differed partly for CH<inline-formula><mml:math id="M90" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M91" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux processing, as detailed in
Appendix A.</p>
      <p id="d1e1103">The 30 min averaged fluxes were quality-checked to detect measurement errors
and to ensure the fulfillment of theoretical assumptions for the application
of the eddy covariance method. Spikes were present in the CO<inline-formula><mml:math id="M92" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time
series, which can be due to weather conditions, fast changes in the
atmosphere's turbulent conditions, or faulty instrumentation. Outliers in the
CO<inline-formula><mml:math id="M93" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux dataset were detected using the median of absolute deviation
from the median (MAD) as described in Papale et al. (2006) using a threshold
<inline-formula><mml:math id="M94" display="inline"><mml:mrow><mml:mi>z</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:math></inline-formula> and with no distinction between day and night. Additionally, CO<inline-formula><mml:math id="M95" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
flux averaging periods were rejected when the number of spikes per half hour
was &gt; 100 (Mammarella et al., 2015) and when skewness and
kurtosis were outside the [<inline-formula><mml:math id="M96" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2,2] and [1,8] ranges (Vickers and Mahrt,
1997), respectively. Required flux stationarity (FST) within the 30 min flux
averaging period was ensured by rejecting each flux value when the FST
criterion as defined by Foken and Wichura (1996) was above 0.3, a strict
criterion that was chosen, given the challenging footprint on the lake side,
to ensure that fluxes represented the surface of interest. The fen part of
the CO<inline-formula><mml:math id="M97" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux dataset was additionally filtered for poorly developed
turbulence (Mauder and Foken, 2006) and <inline-formula><mml:math id="M98" display="inline"><mml:mrow><mml:msup><mml:mi>u</mml:mi><mml:mo>*</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>-filtered (Papale et al.,
2006) with a threshold determined to be 0.1 m s<inline-formula><mml:math id="M99" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> using the online
tool available at
<uri>https://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb</uri>
(Reichstein et al., 2005). The impact of self-heating on the open path
CO<inline-formula><mml:math id="M100" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux measurements (Burba et al., 2008) is a potential issue when
using the LI7500 model, especially for low-flux environments. It could not be
correctly quantified in this study and was thus not applied to avoid a
potentially large systematic error. A rough estimate of the correction
indicated that it could increase the magnitude of the CO<inline-formula><mml:math id="M101" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes by
0.28 <inline-formula><mml:math id="M102" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M103" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M104" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> on average.</p>
      <p id="d1e1238">Quality check and screening of the CH<inline-formula><mml:math id="M105" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux time series included
rejection of averaging periods when the number of spikes per half hour was
&gt; 100. Fluxes were rejected when skewness and kurtosis were
outside the pre-cited range, in winter only, due to the pulse character of
CH<inline-formula><mml:math id="M106" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions during non-winter periods that could be misinterpreted as
faulty raw data due to a high skewness (Jammet et al., 2015). Flux
stationarity within the averaging time period was also ensured by rejecting
values when the FST criterion was above 0.3. Additionally, flux values for
which a time lag was not found within the plausibility time lag window were
rejected (Eugster et al., 2011; Wille et al., 2008). Gaps were initially
present in the flux dataset due to instrument malfunctioning, particularly in
winter, and power cuts (Fig. S6 in the Supplement). After quality check and
filtering, in total 13 474 CH<inline-formula><mml:math id="M107" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes and 11 629 CO<inline-formula><mml:math id="M108" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes were
available for further analysis (Table S1, Fig. S6 in the Supplement). The
data rejection rate was high; eddy covariance studies in lake environments
usually report high rejection rates from quality-check routines (Jonsson et
al., 2008; Mammarella et al., 2015; Nordbo et al., 2011).</p>
</sec>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Flux footprint and partitioning between lake and wetland</title>
      <p id="d1e1284">As in Jammet et al. (2015), the bidirectional wind pattern at the Stordalen
Mire was used to partition the flux dataset into two main wind sectors which
crossed the two different studied ecosystems. To ensure a clear distinction
between the lake and the fen fluxes and the homogeneity of each surface, the
lake sector was conservatively defined as 20–135<inline-formula><mml:math id="M109" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>, and the fen
sector as 210–330<inline-formula><mml:math id="M110" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> (0<inline-formula><mml:math id="M111" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M112" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 360<inline-formula><mml:math id="M113" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> is true north).
Over the study period, 46.2 % of the measured fluxes originated from the
lake sector, 45.7 % of the measured fluxes originated from the fen
sector, and the residual 8.1 % of the measured flux data was excluded,
for being of lower wind speed and originating from mixed sources. Each season
was nevertheless well represented in the flux dataset of each ecosystem (fen
and lake) thanks to regular shifts in wind direction.</p>
      <p id="d1e1330">The flux footprint was calculated using a 2-D model developed by Kljun et
al. (2015). Inputs to the model include turbulence quantities measured at the
tower (friction velocity (<inline-formula><mml:math id="M114" display="inline"><mml:mrow><mml:msup><mml:mi>u</mml:mi><mml:mo>*</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>), standard deviation of cross-wind velocity
(<inline-formula><mml:math id="M115" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), Obukhov length, horizontal wind speed), height of the
boundary layer (derived from the Era-Interim reanalysis product; Dee et al.,
2011), the measurement height and the surface roughness length which was
separately estimated for the lake (0.001 m), and the fen sectors (0.002 m
in winter to a maximum of 0.10 m in summer, accounting for vegetation
growth). Footprints were calculated for each 30 min time step where the
required data were available, and averaged for the periods of interest
(summer and winter).</p>
      <p id="d1e1355">According to the footprint model, most of the flux measured at the tower
(peak fetch) originated from a distance of 38 m on the fen sector and 73 m
on the lake sector, on average during the ice-free season. The lake surface
was within the cumulative 80 % of flux footprint during the ice-free
seasons (Fig. 1). In winter, the footprint model revealed that the 80 %
cumulative footprint, on the lake side, included part of the land in the
middle of the lake (Fig. S1 in the Supplement). This is likely due to the
lower roughness length (snow cover), but also to more stable atmospheric
conditions: the sensible heat flux <inline-formula><mml:math id="M116" display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> is negative during most of the winter
and the atmospheric stability parameter indicated more stable conditions in
winter as compared to summer conditions. Thus, to avoid large contamination
of the land respiration in the winter lake fluxes due to an extended
footprint over the lake shores, the winter fluxes from the lake sector were
only kept for further analysis when the standard deviation of lateral wind
velocity <inline-formula><mml:math id="M117" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi mathvariant="normal">v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M118" display="inline"><mml:mo>≤</mml:mo></mml:math></inline-formula> 1 m s<inline-formula><mml:math id="M119" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Forbrich et al., 2011)
in order to limit lateral contamination of CO<inline-formula><mml:math id="M120" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes into the footprint
area of interest. This removed an additional 3.7 % of the lake CO<inline-formula><mml:math id="M121" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
flux dataset.</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Ancillary measurements</title>
      <p id="d1e1420">Supporting environmental variables were measured at 1 Hz and averaged and
logged every half hour. Temperature probes (T107, Campbell Scientific, Inc.,
UT, USA) were installed in the peat 5 m south-west of the tower at 5, 10,
25, and 50 cm depths. Net radiation at the fen surface was recorded with an
REBS Net Radiometer, model Q7.1 (Campbell Scientific, Inc., UT, USA). Air
temperature used in this study was measured at 2 m height on a mast located
in the middle of the lake (Fig. 1) with a CS215 probe (Campbell Scientific,
Inc., UT, USA). At the same mast, radiation components were measured with a
CNR4 Net Radiometer (Kipp &amp; Zonen, the Netherlands) from which net
radiation at the lake surface was computed. Water temperature in the center
of the lake (Fig. 1) was measured at 10, 30, 50, and 100 cm depths with
intercalibrated HOBO Water Temp Pro v2 loggers (Onset Computer Corporation,
MA, USA). The loggers are suspended on a nylon line from a mooring float,
which stays at the surface throughout the year. The string assembly was
designed so that the bottom sensor at 100 cm depth is in the surface
sediment. Lake surface albedo was computed daily as the midday ratio (10:00
to 13:00 UTC+1) of the shortwave
radiation components, and used in combination with temperature data to
delimit the ice-cover seasons. Air pressure and precipitation were measured
at a weather station 640 m south of the eddy covariance mast.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <?xmltex \opttitle{Gap filling of CH${}_{{4}}$ and CO${}_{{2}}$ flux time series}?><title>Gap filling of CH<inline-formula><mml:math id="M122" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M123" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time series</title>
      <p id="d1e1449">The estimation of annual carbon exchange budgets required filling of the gaps
in the CH<inline-formula><mml:math id="M124" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M125" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time series. When working with highly
skewed flux datasets such as CH<inline-formula><mml:math id="M126" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from lakes (Fig. C1),
integrating the mean flux over the whole time period may lead to important
overestimation. There is as yet no published account of gap filling CH<inline-formula><mml:math id="M127" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
fluxes measured with eddy covariance. In the present study, gap filling of
the CH<inline-formula><mml:math id="M128" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux time series was performed separately on the lake and fen
flux datasets, using artificial neural networks (ANNs) (Moffat et al., 2010;
Papale and Valentini, 2003). ANNs are multivariate, nonlinear regression
models that are fully empirical: the observational data are used to constrain
the model's numerical relationship between the inputs (independent variables,
i.e., environmental drivers) and outputs (dependent variables, i.e., fluxes)
(Moffat et al., 2010). ANNs have been tested and successfully used to
estimate missing values and gap fill CO<inline-formula><mml:math id="M129" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time series measured with
eddy covariance in forests (Moffat et al., 2007; Papale and Valentini, 2003)
or in urban terrain (Järvi et al., 2012) and to gap fill CH<inline-formula><mml:math id="M130" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
emissions in wetlands (Dengel et al., 2013). To our knowledge, we present the
first attempt at using ANNs to gap fill eddy covariance measurements of
CH<inline-formula><mml:math id="M131" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from a lake.</p>
      <p id="d1e1525">Three ANN models were built separately on CH<inline-formula><mml:math id="M132" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the fen,
CH<inline-formula><mml:math id="M133" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the lake, and CO<inline-formula><mml:math id="M134" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions from the fen, on the
hourly scale. Model development followed workflows introduced by Papale and
Valentini (2003), Moffat et al. (2007), and Dengel et al. (2013).
Environmental variables to be included as inputs were selected according to
their physiological relevance to the production and transport of CH<inline-formula><mml:math id="M135" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M136" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> from the surface to the atmosphere, as reported in the literature.
The relevance of the drivers was confirmed by correlation analysis. Input
variables used for each model are reported in Table B1. A further detailed
description of ANN model development can be found in Supplement S1. Gaps in
the measured CH<inline-formula><mml:math id="M137" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M138" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time series were replaced by
predicted values, and the annual sums were computed by integrating the hourly
flux values over time. The performance of the ANN models was assessed by
comparing the predicted values with original observed values over the whole
dataset (Appendix B).</p>
      <p id="d1e1592">The ANN method did not perform well on the lake CO<inline-formula><mml:math id="M139" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux time series,
which comprised a large number of gaps and a high signal-to-noise ratio. ANN
results were thus excluded for the lake CO<inline-formula><mml:math id="M140" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes to avoid introducing
a high and unnecessary uncertainty. Instead, the seasonal lake CO<inline-formula><mml:math id="M141" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
exchange was computed by multiplying the mean flux rate during each season by
the number of days. Considering the normal distribution of the CO<inline-formula><mml:math id="M142" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> lake
fluxes (Fig. C1), this method was considered an acceptable way of filling
missing values.</p>
</sec>
<sec id="Ch1.S2.SS6">
  <title>Uncertainty analysis</title>
      <p id="d1e1637">The total random error is a composite of errors associated with instrument
noise, the stochastic nature of turbulence, the instrument precision, and the
variation of the flux footprint (Moncrieff et al., 1996). The relative random
error increases with the magnitude of the flux (Richardson et al., 2006),
while over time it decreases with increasing size of the dataset because of
its random nature (Moncrieff et al., 1996). It is therefore negligible when
propagated over annual sums, but can be important for single flux values. The
random error was calculated as the sampling error for each flux value in the
flux calculation software using the method of Finkelstein and Sims (2001).</p>
      <p id="d1e1640">The mean random error of the quality-checked measured CH<inline-formula><mml:math id="M143" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes was
2.9 <inline-formula><mml:math id="M144" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 4.3 (mean <inline-formula><mml:math id="M145" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> SD) nmol m<inline-formula><mml:math id="M146" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M147" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at the lake and
4.7 <inline-formula><mml:math id="M148" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 3.8 nmol m<inline-formula><mml:math id="M149" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M150" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at the fen, which corresponds to
7.6 and 6 % of the overall mean measured fluxes, respectively. This is in
the lower end of ranges reported for CO<inline-formula><mml:math id="M151" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and energy fluxes. The mean
random error of the individual measured lake CH<inline-formula><mml:math id="M152" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes was highest in
winter (24 %) and lowest during the thaw season (11 %) when the
largest fluxes were measured. The mean random error of the quality-checked
measured CO<inline-formula><mml:math id="M153" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes was
0.20 <inline-formula><mml:math id="M154" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.57 <inline-formula><mml:math id="M155" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M156" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M157" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at the lake and
0.32 <inline-formula><mml:math id="M158" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.48 <inline-formula><mml:math id="M159" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M160" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M161" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at the fen, equivalent
to 31 and 13 %, respectively, of the overall mean absolute measured flux,
indicating that our setup was able to measure both CH<inline-formula><mml:math id="M162" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M163" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fluxes observable at our site. These values are comparable to what has been
reported in vegetated (Finkelstein and Sims, 2001), urban (Järvi et al.,
2012), boreal lake (Mammarella et al., 2015), and other typical eddy
covariance sites (Rannik et al., 2016). In spring the random error of
CO<inline-formula><mml:math id="M164" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes at the lake was 18 % of the measured flux; however,
during the ice-free season it was above the absolute measured flux in
20 % of the cases. Thus air–lake CO<inline-formula><mml:math id="M165" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange rates during the
summer were low and sometimes close to the detection limit.</p>
      <p id="d1e1863">The random error of the fluxes modeled with ANN (Appendix B) was on average
4 nmol m<inline-formula><mml:math id="M166" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M167" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for fen CH<inline-formula><mml:math id="M168" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes,
0.23 <inline-formula><mml:math id="M169" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M170" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M171" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for fen CO<inline-formula><mml:math id="M172" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes, and
11 nmol m<inline-formula><mml:math id="M173" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M174" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for lake CH<inline-formula><mml:math id="M175" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes. These errors were
small when propagated onto seasonal and annual sums using the random error
propagation principle (Moncrieff et al., 1996). The systematic bias in the
annual flux due to the gap filling method, the bias error (BE), was
calculated on the seasonal and annual flux sums as in Moffat et al. (2007) as
the sum of the difference between the predicted values <inline-formula><mml:math id="M176" display="inline"><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the
observed values <inline-formula><mml:math id="M177" display="inline"><mml:mrow><mml:msub><mml:mi>o</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>:
            <disp-formula id="Ch1.E1" content-type="numbered"><mml:math id="M178" display="block"><mml:mrow><mml:mi mathvariant="normal">BE</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mi>N</mml:mi></mml:mfrac></mml:mstyle><mml:mo movablelimits="false">∑</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>p</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>o</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math id="M179" display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula> is the number of gap filled values in the flux time series. The
bias error adds up over time. It was multiplied by the number of gap filled
values to obtain a total seasonal and annual offset (Moffat et al., 2007).
The offset can be the largest source of uncertainty in the computation of
annual budgets. The systematic offset due to gap filling was larger for
annual CO<inline-formula><mml:math id="M180" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fen fluxes (Table 3), likely because of the higher noise in
the measurements and higher number of gaps during the second year. For total
lake CO<inline-formula><mml:math id="M181" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes, the annual BE was calculated in the same way, using the
seasonal mean as the predicted values. The resulting offset due to gap
filling was close to zero (Table 3), because flux values were normally
distributed, which confirms that using the mean did not induce a significant
bias for this particular dataset.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><caption><p id="d1e2059">Daily mean of air, peat, and surface sediment
temperature <bold>(a)</bold>; cumulative daily precipitation <bold>(b)</bold>; daily
mean net radiation input at the fen and the lake surfaces <bold>(c)</bold>;
albedo of the lake surface <bold>(d)</bold>; daily temperature gradient in the
lake water column defined as (<inline-formula><mml:math id="M182" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi mathvariant="normal">w</mml:mi><mml:mo>,</mml:mo><mml:mn mathvariant="normal">10</mml:mn><mml:mspace width="0.25em" linebreak="nobreak"/><mml:mi mathvariant="normal">cm</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M183" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>
<inline-formula><mml:math id="M184" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi mathvariant="normal">w</mml:mi><mml:mo>,</mml:mo><mml:mn mathvariant="normal">100</mml:mn><mml:mspace linebreak="nobreak" width="0.25em"/><mml:mi mathvariant="normal">cm</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>) divided by the depth difference <inline-formula><mml:math id="M185" display="inline"><mml:mrow><mml:mi mathvariant="normal">Δ</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula>
<bold>(e)</bold>; water temperature profile in the lake center derived from
continuous daily temperature measurements at depths 10 cm, 30 cm, 50 cm,
and 100 cm (<inline-formula><mml:math id="M186" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> bottom) <bold>(f)</bold>. The shaded areas indicate the periods
of ice cover at the lake. PN stands for polar night, i.e., near zero solar
input. The black arrows indicate the estimated time of complete lake overturn
after ice-out.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f02.png"/>

        </fig>

</sec>
<sec id="Ch1.S2.SS7">
  <title>Definition of seasons</title>
      <p id="d1e2155">Observations started in June 2012 and were sustained nearly continuously
until December 2014. We adopted a lake-centric definition of seasons based on
the lake ice phenology. A full year was defined from 1 June to 31 May of the
next year, so that an entire ice-cover season was included in a given year.
This keeps the connected thaw period and previous ice-cover season within the
same year. The year was further divided into an ice-cover season (winter), an
ice-free season (summer and fall), and a thaw season (spring). The thaw
season represents a transitional period during which the snow cover and lake
ice melt. It is separated from summer, since the hydrological and
biogeochemical dynamics in seasonally ice-covered lakes differ from the rest
of the open-water season.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p id="d1e2161">Climatic conditions per season: mean air temperature measured at the
Abisko Scientific Research Station, peat temperature at 10 cm depth in the
fen, surface sediment temperature in the lake (1 m depth), and total
incoming solar radiation (<inline-formula><mml:math id="M187" display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). Season delimitations (see text for a
definition) are reported for each year.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="8">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:colspec colnum="7" colname="col7" align="right"/>
     <oasis:colspec colnum="8" colname="col8" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Season</oasis:entry>  
         <oasis:entry colname="col2">Year</oasis:entry>  
         <oasis:entry colname="col3">Dates</oasis:entry>  
         <oasis:entry colname="col4">Length</oasis:entry>  
         <oasis:entry colname="col5">Air <inline-formula><mml:math id="M188" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6">Peat <inline-formula><mml:math id="M189" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> at</oasis:entry>  
         <oasis:entry colname="col7">Surf. sed.</oasis:entry>  
         <oasis:entry colname="col8">Total <inline-formula><mml:math id="M190" display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">(days)</oasis:entry>  
         <oasis:entry colname="col5">(<inline-formula><mml:math id="M191" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C)</oasis:entry>  
         <oasis:entry colname="col6">10 cm (<inline-formula><mml:math id="M192" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C)</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M193" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math id="M194" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C)</oasis:entry>  
         <oasis:entry colname="col8">(10<inline-formula><mml:math id="M195" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> Wm<inline-formula><mml:math id="M196" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Ice-free</oasis:entry>  
         <oasis:entry colname="col2">2012</oasis:entry>  
         <oasis:entry colname="col3">1 June–14 Oct.</oasis:entry>  
         <oasis:entry colname="col4">136</oasis:entry>  
         <oasis:entry colname="col5">7.8</oasis:entry>  
         <oasis:entry colname="col6">8.9</oasis:entry>  
         <oasis:entry colname="col7">10.2</oasis:entry>  
         <oasis:entry colname="col8">808</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013</oasis:entry>  
         <oasis:entry colname="col3">26 May–15 Oct</oasis:entry>  
         <oasis:entry colname="col4">143</oasis:entry>  
         <oasis:entry colname="col5">10.2</oasis:entry>  
         <oasis:entry colname="col6">9.9</oasis:entry>  
         <oasis:entry colname="col7">12.0</oasis:entry>  
         <oasis:entry colname="col8">902</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2014</oasis:entry>  
         <oasis:entry colname="col3">2 Jun–9 Oct</oasis:entry>  
         <oasis:entry colname="col4">130</oasis:entry>  
         <oasis:entry colname="col5">10.4</oasis:entry>  
         <oasis:entry colname="col6">10.5</oasis:entry>  
         <oasis:entry colname="col7">12.8</oasis:entry>  
         <oasis:entry colname="col8">1019</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Ice-cover</oasis:entry>  
         <oasis:entry colname="col2">2012–2013</oasis:entry>  
         <oasis:entry colname="col3">15 Oct–14 Apr</oasis:entry>  
         <oasis:entry colname="col4">182</oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math id="M197" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>7.9</oasis:entry>  
         <oasis:entry colname="col6">0.0</oasis:entry>  
         <oasis:entry colname="col7">0.7</oasis:entry>  
         <oasis:entry colname="col8">279</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013–2014</oasis:entry>  
         <oasis:entry colname="col3">16 Oct–10 Apr</oasis:entry>  
         <oasis:entry colname="col4">177</oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math id="M198" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>6.5</oasis:entry>  
         <oasis:entry colname="col6">0.2</oasis:entry>  
         <oasis:entry colname="col7">0.8</oasis:entry>  
         <oasis:entry colname="col8">239</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Thaw</oasis:entry>  
         <oasis:entry colname="col2">2013</oasis:entry>  
         <oasis:entry colname="col3">15 Apr–25 May</oasis:entry>  
         <oasis:entry colname="col4">41</oasis:entry>  
         <oasis:entry colname="col5">4.3</oasis:entry>  
         <oasis:entry colname="col6">0.3</oasis:entry>  
         <oasis:entry colname="col7">1.9</oasis:entry>  
         <oasis:entry colname="col8">250</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2014</oasis:entry>  
         <oasis:entry colname="col3">11 Apr–1 Jun</oasis:entry>  
         <oasis:entry colname="col4">52</oasis:entry>  
         <oasis:entry colname="col5">2.2</oasis:entry>  
         <oasis:entry colname="col6">1</oasis:entry>  
         <oasis:entry colname="col7">1.9</oasis:entry>  
         <oasis:entry colname="col8">502</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Annual</oasis:entry>  
         <oasis:entry colname="col2">2012–2013</oasis:entry>  
         <oasis:entry colname="col3">1 Jun–31 May</oasis:entry>  
         <oasis:entry colname="col4">365</oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math id="M199" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.3</oasis:entry>  
         <oasis:entry colname="col6">3.5</oasis:entry>  
         <oasis:entry colname="col7">4.7</oasis:entry>  
         <oasis:entry colname="col8">1424</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013–2014</oasis:entry>  
         <oasis:entry colname="col3">1 Jun–31 May</oasis:entry>  
         <oasis:entry colname="col4">365</oasis:entry>  
         <oasis:entry colname="col5">0.9</oasis:entry>  
         <oasis:entry colname="col6">4</oasis:entry>  
         <oasis:entry colname="col7">5.1</oasis:entry>  
         <oasis:entry colname="col8">1543</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p id="d1e2599">Daily air temperature was used to define seasons. The start of the ice-cover
season was defined as the start of the lake freeze-up, i.e., the first day on
which daily mean air temperature is below zero for 3 consecutive days.
Further, this date coincided each year (2012 to 2014) with the formation of
thermal stratification in the water column (Fig. 2d) due to a rise in bottom
water temperature right after the first day of freezing (Fig. 2a, blue line).
This indicates the inhibition of direct heat exchange between the lake and
the atmosphere when ice forms at the lake surface. In the first year (2012),
the first day of the ice-cover season was confirmed by visual observation of
ice over the whole lake surface, while in the following years, these combined
temperature observations were used to define the start of ice cover.</p>
      <p id="d1e2602">The end of the ice-cover season was defined as the start of thaw, i.e., the
first date on which daily mean air temperature rose above 0 <inline-formula><mml:math id="M200" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for
at least 3 consecutive days. This date preceded by 1 to 2 days the
temperature rise to 0 <inline-formula><mml:math id="M201" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in the surface (10 cm) of the lake ice.
Further, the start of the thaw season could be confirmed by the increase in
mean daily net radiation to net positive values at the lake and the fen
surfaces (Fig. 2c) and by a decrease in lake albedo (Fig. 2d) until
open-water values were reached (mean <inline-formula><mml:math id="M202" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.05). We thereby defined two
complete ice-cover seasons during the study period: from 15 October 2012 to
14 April 2013 (182 days) and from 16 October 2013 to 10 April 2014
(177 days). In 2014, freeze-up of the lake occurred on 10 October. The
ice-cover seasons were systematically characterized by negative daily energy
input at the lake and at the fen (Fig. 2). Thus our season definition based
on daily air temperature was robust and reproducible each year.</p>
      <p id="d1e2631">The end of spring (i.e., the thaw season) and the beginning of the ice-free
season were defined as the first date with a daily temperature gradient in
the water column close to 0 <inline-formula><mml:math id="M203" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C m<inline-formula><mml:math id="M204" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> after the spring overturn,
i.e., when the lake enters its isothermal conditions after complete ice thaw.
The dataset of this study covers 2 complete years plus an additional ice-free
season, i.e., three ice-free seasons, two ice-cover seasons, and two thaw
seasons. Season dates and
lengths are summarized in Table 1.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
<sec id="Ch1.S3.SS1">
  <title>Environmental conditions and lake climatology</title>
      <p id="d1e2667">Mean annual (June to May) air temperature measured at the Abisko Scientific
Research Station was <inline-formula><mml:math id="M205" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.3 <inline-formula><mml:math id="M206" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in 2012–2013 and 0.9 <inline-formula><mml:math id="M207" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in
2013–2014. The latter was significantly above the long-term average
(1913–2014) of <inline-formula><mml:math id="M208" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.5 <inline-formula><mml:math id="M209" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 1 <inline-formula><mml:math id="M210" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (mean <inline-formula><mml:math id="M211" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> SD). The ice-free
season was warmest in 2014 and coolest in 2012 (Table 1). This difference
between years was reflected in both the mean daily peat temperature measured
at 10 cm depth and the mean daily lake water temperatures, which were
warmest in 2014 (Fig. 2; Table 1). The mean air temperature observed over our
study period correlated with total incoming solar radiation, both annually
and during the ice-free periods (Table 1). Winter 2013–2014 was on average
2.1 <inline-formula><mml:math id="M212" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C warmer than the previous one and the ice-cover season was 5
days shorter due to an earlier thaw start. The thaw period started earlier in
2014 but lasted longer (Fig. 2d, Table 1); complete lake overturn (isothermal
water column) following ice thaw occurred 7 days later than in 2013.</p>
      <p id="d1e2735">The development pattern of thermal stratification along lake depth at
freeze-up and its breakdown in spring was similar in both years (Fig. 2d). In
both spring 2013 and 2014, the lake overturn occurred after the development
of strong thermal stratification in the lake during thaw (Fig. 2e, f). The
temperature at the bottom of the lake was up to 4 <inline-formula><mml:math id="M213" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C warmer than the
surface in spring 2013 and up to 6 <inline-formula><mml:math id="M214" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C warmer in 2014, likely
indicating the penetration of solar radiation through thinning ice before
complete ice-out and full water mixing. The thermal structure at the
beginning of freeze-up, as well as during the period of ice thaw preceding
spring overturn in 2013, has been previously described in detail for this
site in a winter-focused study (Jammet et al., 2015).</p>
      <p id="d1e2756">During the ice-free, summer season, there was slight to no thermal
stratification in the water column (Fig. 2d). The shallow lake water column
reacted quickly to temperature changes (Fig. 2a, d) and the dark bottom
warmed up quickly since solar radiation can reach the sediment surface. Thus,
the lake had a polymictic behavior; i.e., it was regularly mixing to the
bottom during the ice-free season, which ensures isothermal conditions in the
water column throughout the summer. Water temperature reached a maximum of
23.8 <inline-formula><mml:math id="M215" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in July 2014. Conversely, a strong temperature gradient
formed during winter (Fig. 2f). In both winters the surface sediment
temperature dropped below 0 <inline-formula><mml:math id="M216" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C by February, with minima of
<inline-formula><mml:math id="M217" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.9 <inline-formula><mml:math id="M218" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in March 2013 and <inline-formula><mml:math id="M219" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.6 <inline-formula><mml:math id="M220" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in February 2014.
This suggests that the water column froze to the bottom. The temperatures in
the peat soil and at the surface sediment in the lake were de-coupled from
air temperature (Fig. 2a), showing the hindrance of heat exchange with the
atmosphere due to the presence of ice and snow at the surface.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p id="d1e2813">Statistical exploration of the lake flux dataset: Spearman's rank
correlation coefficient (<inline-formula><mml:math id="M221" display="inline"><mml:mrow><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> shows the degree of association between
half-hourly lake CH<inline-formula><mml:math id="M222" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux and lake CO<inline-formula><mml:math id="M223" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux with potential drivers
of variability. All data were grouped per season. See Table 1 for the
limitation of the seasons. Lake fluxes are filtered in winter for high
standard deviation of lateral wind speed.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="10">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:colspec colnum="6" colname="col6" align="center"/>
     <oasis:colspec colnum="7" colname="col7" align="right"/>
     <oasis:colspec colnum="8" colname="col8" align="right"/>
     <oasis:colspec colnum="9" colname="col9" align="right"/>
     <oasis:colspec colnum="10" colname="col10" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry rowsep="1" namest="col2" nameend="col5" align="center">Lake CH<inline-formula><mml:math id="M230" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux (Spearman's <inline-formula><mml:math id="M231" display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula>) </oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry rowsep="1" namest="col7" nameend="col10" align="center">Lake CO<inline-formula><mml:math id="M232" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux (Spearman's <inline-formula><mml:math id="M233" display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula>) </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Annual</oasis:entry>  
         <oasis:entry colname="col3">Ice-free</oasis:entry>  
         <oasis:entry colname="col4">Thaw</oasis:entry>  
         <oasis:entry colname="col5">Ice-cover</oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7">Annual</oasis:entry>  
         <oasis:entry colname="col8">Ice-free</oasis:entry>  
         <oasis:entry colname="col9">Thaw</oasis:entry>  
         <oasis:entry colname="col10">Ice-cover</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Air <inline-formula><mml:math id="M234" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2">0.36<inline-formula><mml:math id="M235" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.40<inline-formula><mml:math id="M236" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.26<inline-formula><mml:math id="M237" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.14<inline-formula><mml:math id="M238" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M239" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.21<inline-formula><mml:math id="M240" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8"><inline-formula><mml:math id="M241" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.22<inline-formula><mml:math id="M242" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.38<inline-formula><mml:math id="M243" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.16<inline-formula><mml:math id="M244" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math id="M245" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> water surface</oasis:entry>  
         <oasis:entry colname="col2">0.27<inline-formula><mml:math id="M246" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.48<inline-formula><mml:math id="M247" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.37<inline-formula><mml:math id="M248" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.18<inline-formula><mml:math id="M249" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M250" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.21<inline-formula><mml:math id="M251" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8"><inline-formula><mml:math id="M252" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.21<inline-formula><mml:math id="M253" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.27<inline-formula><mml:math id="M254" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.09<inline-formula><mml:math id="M255" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math id="M256" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> bottom</oasis:entry>  
         <oasis:entry colname="col2">0.24<inline-formula><mml:math id="M257" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.49<inline-formula><mml:math id="M258" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.49<inline-formula><mml:math id="M259" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.10<inline-formula><mml:math id="M260" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M261" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.26<inline-formula><mml:math id="M262" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8"><inline-formula><mml:math id="M263" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.21<inline-formula><mml:math id="M264" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.40<inline-formula><mml:math id="M265" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M266" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.10<inline-formula><mml:math id="M267" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Wind speed</oasis:entry>  
         <oasis:entry colname="col2">0.36<inline-formula><mml:math id="M268" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.32<inline-formula><mml:math id="M269" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.40<inline-formula><mml:math id="M270" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.27<inline-formula><mml:math id="M271" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7">0.26<inline-formula><mml:math id="M272" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8">0.13<inline-formula><mml:math id="M273" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.38<inline-formula><mml:math id="M274" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10">0.36<inline-formula><mml:math id="M275" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">H flux</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math id="M276" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.15<inline-formula><mml:math id="M277" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.12<inline-formula><mml:math id="M278" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M279" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.18<inline-formula><mml:math id="M280" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math id="M281" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.12<inline-formula><mml:math id="M282" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M283" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.62<inline-formula><mml:math id="M284" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8"><inline-formula><mml:math id="M285" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.67<inline-formula><mml:math id="M286" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M287" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.38<inline-formula><mml:math id="M288" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M289" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.50<inline-formula><mml:math id="M290" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">LE flux</oasis:entry>  
         <oasis:entry colname="col2">0.24<inline-formula><mml:math id="M291" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.38<inline-formula><mml:math id="M292" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.16<inline-formula><mml:math id="M293" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.08</oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7">-0.29<inline-formula><mml:math id="M294" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8">-0.49<inline-formula><mml:math id="M295" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.05</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M296" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.14<inline-formula><mml:math id="M297" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Solar radiation</oasis:entry>  
         <oasis:entry colname="col2">0.27<inline-formula><mml:math id="M298" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.13<inline-formula><mml:math id="M299" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M300" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.02</oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math id="M301" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.11<inline-formula><mml:math id="M302" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M303" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.09<inline-formula><mml:math id="M304" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col8"><inline-formula><mml:math id="M305" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.52<inline-formula><mml:math id="M306" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col9">0.02</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M307" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.22<inline-formula><mml:math id="M308" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CO<inline-formula><mml:math id="M309" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux</oasis:entry>  
         <oasis:entry colname="col2">0.41<inline-formula><mml:math id="M310" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math id="M311" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.13<inline-formula><mml:math id="M312" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.67<inline-formula><mml:math id="M313" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.21<inline-formula><mml:math id="M314" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"/>  
         <oasis:entry colname="col7">–</oasis:entry>  
         <oasis:entry colname="col8">–</oasis:entry>  
         <oasis:entry colname="col9">–</oasis:entry>  
         <oasis:entry colname="col10">–</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p id="d1e2844"><inline-formula><mml:math id="M224" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M225" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>-value &lt; 0.1;
<inline-formula><mml:math id="M226" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M227" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>-value &lt; 0.01;
<inline-formula><mml:math id="M228" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>*</mml:mo><mml:mo>*</mml:mo><mml:mo>*</mml:mo></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M229" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>-value &lt; 0.001.</p></table-wrap-foot></table-wrap>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><caption><p id="d1e4137">Measured CH<inline-formula><mml:math id="M315" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M316" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes at the fen <bold>(a, b)</bold> and
the lake <bold>(c, d)</bold> over the full study period. Light grey dots are
half-hourly values and black dots show a 5-day running mean. Note on
panel <bold>(c)</bold>: nine flux values above 800 nmol m<inline-formula><mml:math id="M317" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M318" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> are
not displayed for visibility.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f03.png"/>

        </fig>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3" specific-use="star"><caption><p id="d1e4201">Seasonal and annual sums of CO<inline-formula><mml:math id="M319" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M320" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes after gap
filling, in g C m<inline-formula><mml:math id="M321" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M322" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Sum BE is the bias due to the gap
filling model (Eq. 1), scaled to annual flux units and multiplied by the
number of gaps in the flux dataset over the season or year. The sum of
CO<inline-formula><mml:math id="M323" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from the lake is only reported for the first year.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.97}[.97]?><oasis:tgroup cols="13">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="center"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:colspec colnum="7" colname="col7" align="right"/>
     <oasis:colspec colnum="8" colname="col8" align="center"/>
     <oasis:colspec colnum="9" colname="col9" align="right"/>
     <oasis:colspec colnum="10" colname="col10" align="right"/>
     <oasis:colspec colnum="11" colname="col11" align="center"/>
     <oasis:colspec colnum="12" colname="col12" align="right"/>
     <oasis:colspec colnum="13" colname="col13" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry rowsep="1" namest="col3" nameend="col4" align="center">Fen CH<inline-formula><mml:math id="M325" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux </oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry rowsep="1" namest="col6" nameend="col7" align="center">Lake CH<inline-formula><mml:math id="M326" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux </oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry rowsep="1" namest="col9" nameend="col10" align="center">Fen CO<inline-formula><mml:math id="M327" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux </oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry rowsep="1" namest="col12" nameend="col13" align="center">Lake CO<inline-formula><mml:math id="M328" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Season</oasis:entry>  
         <oasis:entry colname="col2">Year</oasis:entry>  
         <oasis:entry colname="col3">Total flux</oasis:entry>  
         <oasis:entry colname="col4">Sum BE</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">Total flux</oasis:entry>  
         <oasis:entry colname="col7">Sum BE</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">Total flux</oasis:entry>  
         <oasis:entry colname="col10">Sum BE</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">Total flux</oasis:entry>  
         <oasis:entry colname="col13">Sum BE</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Ice-free</oasis:entry>  
         <oasis:entry colname="col2">2012</oasis:entry>  
         <oasis:entry colname="col3">14.8</oasis:entry>  
         <oasis:entry colname="col4">0.1</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">2.5</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M329" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.1</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M330" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>179.4</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M331" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>14.8</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12"><inline-formula><mml:math id="M332" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>24.4</oasis:entry>  
         <oasis:entry colname="col13">&lt; 0.001</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013</oasis:entry>  
         <oasis:entry colname="col3">16.2</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M333" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.1</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">2.8</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M334" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.1</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M335" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>201.3</oasis:entry>  
         <oasis:entry colname="col10">13.2</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">nc<inline-formula><mml:math id="M336" display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col13">nc</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2014</oasis:entry>  
         <oasis:entry colname="col3">16.8</oasis:entry>  
         <oasis:entry colname="col4">0.09</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">3.0</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M337" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.5</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M338" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>239.6</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M339" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>5.1</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">nc</oasis:entry>  
         <oasis:entry colname="col13">nc</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Ice-cover</oasis:entry>  
         <oasis:entry colname="col2">2012–2013</oasis:entry>  
         <oasis:entry colname="col3">4.1</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M340" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.2</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">0.3</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M341" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.3</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">109.6</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M342" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>8.8</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">12.4</oasis:entry>  
         <oasis:entry colname="col13">&lt; 0.001</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013–2014</oasis:entry>  
         <oasis:entry colname="col3">4.2</oasis:entry>  
         <oasis:entry colname="col4">0.7</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">0.4</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M343" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.4</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">115.5</oasis:entry>  
         <oasis:entry colname="col10">20.7</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">nc</oasis:entry>  
         <oasis:entry colname="col13">nc</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Thaw</oasis:entry>  
         <oasis:entry colname="col2">2013</oasis:entry>  
         <oasis:entry colname="col3">1.4</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M344" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.1</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">2.5</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M345" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.2</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">11.3</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M346" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.4</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">33.3</oasis:entry>  
         <oasis:entry colname="col13">&lt; 0.001</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2014</oasis:entry>  
         <oasis:entry colname="col3">1.7</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M347" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.07</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">1.3</oasis:entry>  
         <oasis:entry colname="col7">0.5</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9">11.7</oasis:entry>  
         <oasis:entry colname="col10">1.1</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">nc</oasis:entry>  
         <oasis:entry colname="col13">nc</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Annual</oasis:entry>  
         <oasis:entry colname="col2">2012–2013</oasis:entry>  
         <oasis:entry colname="col3">20.3</oasis:entry>  
         <oasis:entry colname="col4">0.2</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">5.3</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M348" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.9</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M349" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>58.5</oasis:entry>  
         <oasis:entry colname="col10"><inline-formula><mml:math id="M350" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>26.1</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">21.5</oasis:entry>  
         <oasis:entry colname="col13">&lt; 0.001</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">2013–2014</oasis:entry>  
         <oasis:entry colname="col3">22.1</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M351" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.1</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">4.4</oasis:entry>  
         <oasis:entry colname="col7">0.6</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M352" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>74.1</oasis:entry>  
         <oasis:entry colname="col10">97.4</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">nc</oasis:entry>  
         <oasis:entry colname="col13">nc</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Annual</oasis:entry>  
         <oasis:entry colname="col2">Average <inline-formula><mml:math id="M353" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> SD</oasis:entry>  
         <oasis:entry colname="col3">21.2 <inline-formula><mml:math id="M354" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 1.3</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M355" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.2</oasis:entry>  
         <oasis:entry colname="col5"/>  
         <oasis:entry colname="col6">4.9 <inline-formula><mml:math id="M356" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.6</oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math id="M357" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.7</oasis:entry>  
         <oasis:entry colname="col8"/>  
         <oasis:entry colname="col9"><inline-formula><mml:math id="M358" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>66.3 <inline-formula><mml:math id="M359" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 11</oasis:entry>  
         <oasis:entry colname="col10">35.7</oasis:entry>  
         <oasis:entry colname="col11"/>  
         <oasis:entry colname="col12">21.5</oasis:entry>  
         <oasis:entry colname="col13">&lt; 0.001</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table><?xmltex \begin{scaleboxenv}{.97}[.97]?><table-wrap-foot><p id="d1e4255"><inline-formula><mml:math id="M324" display="inline"><mml:msup><mml:mi/><mml:mo>∗</mml:mo></mml:msup></mml:math></inline-formula> nc: not computed.</p></table-wrap-foot><?xmltex \end{scaleboxenv}?></table-wrap>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p id="d1e5008">Measured flux rates of CH<inline-formula><mml:math id="M360" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> <bold>(a)</bold> and
CO<inline-formula><mml:math id="M361" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> <bold>(b)</bold> per season and per ecosystem. The central line of the
boxplots shows the median, box edges show the 25th and 75th percentiles, and
whiskers show the 5th and 95th percentiles. The black dots indicate the mean
flux rate. Outliers are not displayed.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f04.png"/>

        </fig>

</sec>
<sec id="Ch1.S3.SS2">
  <?xmltex \opttitle{Year-round CH${}_{{4}}$ and CO${}_{{2}}$ fluxes}?><title>Year-round CH<inline-formula><mml:math id="M362" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M363" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes</title>
      <p id="d1e5066">CH<inline-formula><mml:math id="M364" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the lake showed a highly skewed distribution
(Fig. C1a); there was a large difference between the overall mean
(40 nmol m<inline-formula><mml:math id="M365" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M366" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) and overall median
(12 nmol m<inline-formula><mml:math id="M367" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M368" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). The seasonal flux pattern was characterized
by low background emissions and occasional, large degassing events (Fig. 3)
with 25 % of measured data above 111 nmol m<inline-formula><mml:math id="M369" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M370" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the
thaw period, and 5 % of measured data above 75 nmol m<inline-formula><mml:math id="M371" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M372" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
within the ice-free season (Fig. 4). Over the full measurement period, summer
emission rates averaged to 26 nmol m<inline-formula><mml:math id="M373" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M374" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
12 nmol m<inline-formula><mml:math id="M375" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M376" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), spring emission rates to
84 nmol m<inline-formula><mml:math id="M377" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M378" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median 33 nmol m<inline-formula><mml:math id="M379" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M380" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), and
winter emissions to 2.8 nmol m<inline-formula><mml:math id="M381" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M382" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
3.0 nmol m<inline-formula><mml:math id="M383" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M384" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). The mean and median of the winter emissions
were not significantly different from the mean random error of the fluxes.
CO<inline-formula><mml:math id="M385" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes were close to normally distributed at the lake (Fig. C1b) and
the overall mean rate was 0.22 <inline-formula><mml:math id="M386" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol CO<inline-formula><mml:math id="M387" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M388" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M389" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(median 0.18 <inline-formula><mml:math id="M390" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M391" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M392" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). There was a distinctive
CO<inline-formula><mml:math id="M393" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> outgassing at the time of water overturn during the spring of both
2013 and 2014 (Fig. 3d). The mean measured CO<inline-formula><mml:math id="M394" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange at the lake was
significantly negative during the ice-free seasons (one sample <inline-formula><mml:math id="M395" display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula>-test,
<inline-formula><mml:math id="M396" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.001), <inline-formula><mml:math id="M397" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.14 <inline-formula><mml:math id="M398" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M399" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M400" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>,
indicating a low net uptake of CO<inline-formula><mml:math id="M401" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (Fig. 4). Negative flux rates started
right after the spring CO<inline-formula><mml:math id="M402" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> outgassing in 2013 and 2014 (Fig. 3d). The
highest CO<inline-formula><mml:math id="M403" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake rates were observed during the summer of 2014, which
was the warmest summer of the study period, with the highest solar radiation
input (Table 1). In fall 2014, a burst of CO<inline-formula><mml:math id="M404" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> was measured at the lake,
which was not present in previous years (Fig. 3d). This fall burst was not
observed in the CH<inline-formula><mml:math id="M405" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux measurements. Wintertime CO<inline-formula><mml:math id="M406" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions
from the lake were significantly above the flux random error and
significantly positive (Figs. 3d, 4). There was an inter-annual variability
in the magnitude of the CH<inline-formula><mml:math id="M407" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> spring degassing from the lake between the 2
years (Fig. 3c). In contrast, mean CO<inline-formula><mml:math id="M408" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> degassing was higher during the
second thaw season, 0.78 <inline-formula><mml:math id="M409" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol CO<inline-formula><mml:math id="M410" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M411" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M412" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
0.47 <inline-formula><mml:math id="M413" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol CO<inline-formula><mml:math id="M414" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M415" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M416" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) in 2013 and
0.99 <inline-formula><mml:math id="M417" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol CO<inline-formula><mml:math id="M418" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M419" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M420" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
0.75 <inline-formula><mml:math id="M421" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol CO<inline-formula><mml:math id="M422" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M423" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M424" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) in 2014. Both CH<inline-formula><mml:math id="M425" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M426" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions during spring were significantly higher than during the
following ice-free season, in both years (Fig. S2 in the Supplement).</p>
      <p id="d1e5728">The distribution of CH<inline-formula><mml:math id="M427" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the fen was less skewed
(Fig. C1a) and the overall measured mean was 77 nmol m<inline-formula><mml:math id="M428" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M429" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(median 58 nmol m<inline-formula><mml:math id="M430" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M431" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). The highest CH<inline-formula><mml:math id="M432" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions at the
fen occurred during the ice-free season (Fig. 3), with a mean rate of
110 nmol m<inline-formula><mml:math id="M433" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M434" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median 108 nmol m<inline-formula><mml:math id="M435" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M436" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>).
Sustained CH<inline-formula><mml:math id="M437" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions were measured at the fen throughout the winter
(Fig. 3), with a mean rate of 25 nmol m<inline-formula><mml:math id="M438" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M439" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
25 nmol m<inline-formula><mml:math id="M440" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M441" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). Flux rates during the snowmelt and thaw season
averaged to 35 nmol m<inline-formula><mml:math id="M442" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M443" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
33 nmol m<inline-formula><mml:math id="M444" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M445" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). CO<inline-formula><mml:math id="M446" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from the fen averaged to
<inline-formula><mml:math id="M447" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.3 <inline-formula><mml:math id="M448" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M449" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M450" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (median
0.2 <inline-formula><mml:math id="M451" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M452" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M453" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) over the full period, and the mean
rate was <inline-formula><mml:math id="M454" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2.6 <inline-formula><mml:math id="M455" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M456" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M457" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> during the ice-free
seasons. CO<inline-formula><mml:math id="M458" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> respiration was sustained throughout winter (Fig. 3b) at a
mean rate of 0.8 <inline-formula><mml:math id="M459" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M460" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M461" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, and the release of
CO<inline-formula><mml:math id="M462" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> during the melt season was low (Fig. 4).</p>

      <?xmltex \floatpos{p}?><fig id="Ch1.F5"><caption><p id="d1e6123">Averaged seasonality of CO<inline-formula><mml:math id="M463" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M464" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes in both
ecosystems. Dots show daily means across the whole measurement period; lines
are a smoothing filter of the daily mean with a 30-day window. Dashed lines
show the standard deviation around the daily means, smoothed with a 30-day
window.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f05.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p id="d1e6153">CH<inline-formula><mml:math id="M465" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions at the lake during the ice-free seasons of 2012,
2013, and 2014, from day 152 to day 290. Grey dots are half-hourly eddy
covariance observations, open black dots are daily means of the eddy
covariance fluxes, and red dots show spatially averaged daily CH<inline-formula><mml:math id="M466" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
ebullition measured in the lake with bubble traps. Atmospheric pressure
(black line), and water temperature at depths 10 cm (red line) and 100 cm
(sediment surface, blue line) are also shown.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f06.png"/>

        </fig>

      <p id="d1e6180">The average annual seasonality of CH<inline-formula><mml:math id="M467" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M468" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes in both
ecosystems is shown in Fig. 5. The lake dominated CH<inline-formula><mml:math id="M469" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M470" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
emissions during spring. During the ice-free seasons, by contrast, the lake
was a lower emitter of CH<inline-formula><mml:math id="M471" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> than the fen per unit area, and its CO<inline-formula><mml:math id="M472" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
exchange was close to neutral with a small uptake. There was a slight
seasonality in CH<inline-formula><mml:math id="M473" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> lake emissions during summer but, annually, CH<inline-formula><mml:math id="M474" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
and CO<inline-formula><mml:math id="M475" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> lake fluxes peaked in spring (Fig. 5). CH<inline-formula><mml:math id="M476" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from
the fen peaked in August and net CO<inline-formula><mml:math id="M477" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange peaked in July (Fig. 5).
The emission of both gases occurred at lower rates but continuously in
winter.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <title>Variability of lake–air carbon exchange within seasons</title>
      <p id="d1e6289">The thaw and ice-free periods are different in terms of flux dynamics. The
dataset was therefore separated into seasons to explore controls on the lake
fluxes. During the ice-free seasons, half-hourly CH<inline-formula><mml:math id="M478" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes at the lake
were characterized by degassing events that coincided with drops in
atmospheric pressure (Fig. 6). Daily EC flux data were compared with
spatially averaged, daily ebullition fluxes measured in the lake with
ebullition traps located nearby or within the tower footprint. The degassing
events measured with the eddy covariance system coincided in timing and in
magnitude with the daily ebullition fluxes measured with the ebullition traps
(Fig. 6).</p>
      <p id="d1e6301">Due to the high skewness of the CH<inline-formula><mml:math id="M479" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> lake flux dataset (Fig. C1) and the
presence of outliers in both CO<inline-formula><mml:math id="M480" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M481" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux datasets from the
lake, we used Spearman's <inline-formula><mml:math id="M482" display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula> coefficient, which is a statistical measure
of association that is robust to outliers and applicable to skewed
distribution (Kowalski, 1972), to explore bivariate associations. Among
potential flux drivers, the highest correlation of ice-free CH<inline-formula><mml:math id="M483" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
emissions was found with surface sediment temperature (<inline-formula><mml:math id="M484" display="inline"><mml:mrow><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.49</mml:mn></mml:mrow></mml:math></inline-formula>,
Table 2). Degassing events occurred often after an increase in surface
sediment temperature (Fig. 6). When averaging all 30 min CH<inline-formula><mml:math id="M485" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes
during the three ice-free seasons per bins of 1 <inline-formula><mml:math id="M486" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, an exponential
regression between lake CH<inline-formula><mml:math id="M487" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes and surface sediment temperature
could explain 82 % of the variability in CH<inline-formula><mml:math id="M488" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions (Fig. 7).</p>

      <?xmltex \floatpos{p}?><fig id="Ch1.F7"><caption><p id="d1e6398">Relationship between lake CH<inline-formula><mml:math id="M489" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions and surface sediment
temperature during summer, using all half-hourly CH<inline-formula><mml:math id="M490" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux rates averaged
by bins of 1 <inline-formula><mml:math id="M491" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C across the three ice-free seasons. Error bars show
the standard deviation of the CH<inline-formula><mml:math id="M492" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux rates around the means within
each averaging bin. The red line is a regression fit with <inline-formula><mml:math id="M493" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M494" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.82
(<inline-formula><mml:math id="M495" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.001).</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f07.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8" specific-use="star"><caption><p id="d1e6472">Diel medians, mean and 25th–75th percentiles of CH<inline-formula><mml:math id="M496" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes,
CO<inline-formula><mml:math id="M497" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes, sensible heat flux (<inline-formula><mml:math id="M498" display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula>) and latent heat flux (LE) measured
at the lake <bold>(a)</bold> and at the fen <bold>(b)</bold> from June to August over
the three ice-free seasons.</p></caption>
          <?xmltex \igopts{width=426.791339pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f08.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9"><caption><p id="d1e6514">Diel median of the net CO<inline-formula><mml:math id="M499" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange at the fen (red) and at the
lake (blue) vs. diel median solar radiation, between June and August. Each
dot is the hourly median flux of the combined three ice-free seasons. Note
that the two <inline-formula><mml:math id="M500" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> axes have different scales.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f09.png"/>

        </fig>

      <p id="d1e6539">Wind speed correlated best with CH<inline-formula><mml:math id="M501" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> lake emissions during the thaw
period (Table 2, <inline-formula><mml:math id="M502" display="inline"><mml:mrow><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.40</mml:mn></mml:mrow></mml:math></inline-formula>). The relationship was weaker during the
open-water period. We observed a few CH<inline-formula><mml:math id="M503" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> degassing events in summer that
coincided with the likely mixing of the water column following a short period
of thermal stratification (0.8 to 1 <inline-formula><mml:math id="M504" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C gradient between 10 and
100 cm depths, Fig. S3a, b in the Supplement), but these were not systematic
(Fig. S3c, d in the Supplement). During the ice-free season, there was a weak
anti-correlation between CO<inline-formula><mml:math id="M505" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange at the lake and air and water
temperature (Table 2). Wind speed correlated weakly with CO<inline-formula><mml:math id="M506" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> lake
exchange, while there was a strong anti-correlation with sensible heat flux
at the lake surface (Table 2), and with solar radiation input (Table 2).</p>
      <p id="d1e6600">During the thaw seasons, half-hourly CO<inline-formula><mml:math id="M507" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes strongly correlated with
CH<inline-formula><mml:math id="M508" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions (<inline-formula><mml:math id="M509" display="inline"><mml:mrow><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.67</mml:mn></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M510" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.001, Table 2) and
followed the same emission pattern at the half-hourly scale, in both 2013 and
2014 (Fig. S4 in the Supplement). This correlation was not sustained during
the open-water seasons, when the two flux datasets had a very different
short-term variability. Both CH<inline-formula><mml:math id="M511" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M512" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> degassing in spring
positively correlated with increasing air temperature.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10" specific-use="star"><caption><p id="d1e6661">Evaluation of the artificial neural network models: measured vs.
predicted hourly flux values for fen CH<inline-formula><mml:math id="M513" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes <bold>(a)</bold>, lake
CH<inline-formula><mml:math id="M514" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes <bold>(b)</bold>, and fen CO<inline-formula><mml:math id="M515" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes <bold>(c)</bold>. In red is
the <inline-formula><mml:math id="M516" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> line.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f10.png"/>

        </fig>

      <p id="d1e6720">The diurnal course of CO<inline-formula><mml:math id="M517" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, CH<inline-formula><mml:math id="M518" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, and turbulent energy fluxes at the
lake and the fen was calculated on hourly fluxes. Only days with more than
75 % of hourly data coverage were selected. The median flux of each hour
was then computed across all days within each year during the open-water
season, and plotted along with the 25th and 75th percentiles (Fig. 8). There
was no diel cycle visible in the fen CH<inline-formula><mml:math id="M519" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes, while net CO<inline-formula><mml:math id="M520" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
exchange at the fen surface showed a clear peak uptake at noon. Lake methane
fluxes tended to be higher fluxes in the morning hours. A systematic diel
pattern was observed in the lake CO<inline-formula><mml:math id="M521" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes during each open-water
season (Fig. 8), with a slight peak in the mornings in 2012 and 2013, while
CO<inline-formula><mml:math id="M522" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake peaked in the middle of the day in 2014. The 24 h cycle of
sensible heat flux (<inline-formula><mml:math id="M523" display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula>) at the lake peaked in the late morning (Fig. 8) at
ca. 10:00 LT (median 20 W m<inline-formula><mml:math id="M524" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), while
being &lt; 10 W m<inline-formula><mml:math id="M525" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the afternoon. The diel CO<inline-formula><mml:math id="M526" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> pattern
at the lake also coincided with daily variation in water surface and air
temperature and was in antiphase with the diel pattern of sensible heat flux.
Latent heat flux (LE) at the lake peaked in the afternoon. At the hourly
timescale, solar radiation could explain 88 % of the diel variability in
air–lake CO<inline-formula><mml:math id="M527" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange during the summer months (Fig. 9). This light
response curve resembled the one measured at the fen, although less
pronounced.</p>
</sec>
<sec id="Ch1.S3.SS4">
  <title>Annual atmospheric carbon budget</title>
<sec id="Ch1.S3.SS4.SSS1">
  <title>Performance of the ANN modeling</title>
      <p id="d1e6838">The ANN gap filling method was most performant on the fen dataset, achieving
an <inline-formula><mml:math id="M528" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.88 during the training phase, and an <inline-formula><mml:math id="M529" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.85 between
measured and predicted values over the whole dataset (expressing the capacity
of generalization of the model) with a relative mean square error (RMSE) of
23 % (Fig. 10). The ANN gap filling of lake CH<inline-formula><mml:math id="M530" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes achieved an
<inline-formula><mml:math id="M531" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.71 in the training phase and an <inline-formula><mml:math id="M532" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.70 between
predicted and measured fluxes on the whole dataset, with an RMSE of 51 %.
The lake model was most accurate for periods with the best data coverage in
the measured dataset (spring seasons, <inline-formula><mml:math id="M533" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.77</mml:mn></mml:mrow></mml:math></inline-formula>). The lower accuracy of
the model during the ice-free seasons (<inline-formula><mml:math id="M534" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.47</mml:mn></mml:mrow></mml:math></inline-formula>) is also due to the
pulse character of lake ebullition, which was not always reproduced by the
model, while the background seasonal trend was present.</p>
      <p id="d1e6925">For the fen CH<inline-formula><mml:math id="M535" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes, the model was most accurate during the ice-free
seasons when fen CH<inline-formula><mml:math id="M536" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions are tightly linked to peat temperature
and least performant during the thaw periods. Unsurprisingly, the prediction
performance of the models was dependent on data coverage in the original
dataset, but also on the accuracy of the choice of environmental drivers. On
the annual scale, both fen and lake models were most performant during the
first year (June–May), which had the least amount of data loss, with an
<inline-formula><mml:math id="M537" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.88 (RMSE 23 %) in the first year for the fen model and of
0.82 (RMSE 40 %) for the lake model between predicted and measured
fluxes.</p>
      <p id="d1e6957">The ANN modeling was likewise performant on the fen CO<inline-formula><mml:math id="M538" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux dataset,
achieving an <inline-formula><mml:math id="M539" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> of 0.86 (RMSE 35 %) over the whole dataset between
measured and predicted values (Fig. 10). The model was most performant during
the ice-free seasons. This can be explained by a better data coverage but
also by better constrained processes during the growing season and on the
annual scale than during the snow-cover season, when additional drivers than
the one selected as model inputs may play a role in the variability of the
fluxes at the hourly scale (e.g., sensitivity to footprint changes,
turbulence, variation in snow depth, partial melt).</p>
</sec>
<sec id="Ch1.S3.SS4.SSS2">
  <title>Annual and seasonal sums</title>
      <p id="d1e6986">We report seasonal emissions for all available seasons, and for lake CO<inline-formula><mml:math id="M540" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
total annual emissions for the first year only (June 2012 to May 2013), due
to the absence of a robust gap filling model for the second year when data
coverage was lower. During the ice-free seasons, total lake CO<inline-formula><mml:math id="M541" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux was
negative and total lake CH<inline-formula><mml:math id="M542" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux was positive (Table 3). Annually, the
largest contribution to total carbon exchange at the lake was during the
spring season, whereas the ice-free season was quantitatively the most
important period for the annual carbon exchange at the fen (Table 3). On
average over both years, the ice-cover season accounted for 33 % of the
fen annual carbon (CH<inline-formula><mml:math id="M543" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> <inline-formula><mml:math id="M544" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> CO<inline-formula><mml:math id="M545" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) exchange per m<inline-formula><mml:math id="M546" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>. During the first
year, the lake C-emissions equaled 70 % of the total net fen C-exchange.
On a carbon mass basis, CO<inline-formula><mml:math id="M547" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange dominated the total carbon budget.
Total net annual carbon exchange (CH<inline-formula><mml:math id="M548" display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub><mml:mo>+</mml:mo></mml:mrow></mml:math></inline-formula>CO<inline-formula><mml:math id="M549" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) at the fen was
<inline-formula><mml:math id="M550" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>38.2 g C m<inline-formula><mml:math id="M551" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the first year and <inline-formula><mml:math id="M552" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>52 g C m<inline-formula><mml:math id="M553" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the
second year (average <inline-formula><mml:math id="M554" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>45.1 g C m<inline-formula><mml:math id="M555" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M556" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), while the lake
total carbon exchange was positive at 26.7 g C m<inline-formula><mml:math id="M557" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M558" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (first
year only), of which 80 % was emitted as CO<inline-formula><mml:math id="M559" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <title>Contrasting annual seasonality of carbon fluxes between lakes and fens</title>
      <p id="d1e7198">The average annual seasonality of the fluxes across the study period (Fig. 5)
shows that both ecosystems had different peak timings in terms of CH<inline-formula><mml:math id="M560" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
and CO<inline-formula><mml:math id="M561" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange. CH<inline-formula><mml:math id="M562" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the fen followed the expected
seasonality of emissions from boreal and subarctic wetlands (Hargreaves et
al., 2001; Jackowicz-Korczyński et al., 2010; Rinne et al., 2007). The
dense emergent vegetation cover at the waterlogged fen dominated by vascular
plants, which are efficient conduits for CH<inline-formula><mml:math id="M563" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> to reach the atmosphere,
led to maximum primary production of organic carbon during the summer. The
continuous emission of CH<inline-formula><mml:math id="M564" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M565" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> through snow during the winter
season is an important feature of the annual flux cycle. Unlike the ice cover
at the lake, which is complete, stems and branches sticking out of the snow
at the fen site allow a sustained connection with the atmosphere. This limits
the trapping and the buildup of CH<inline-formula><mml:math id="M566" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> under snow during winter. A previous
study showed that CH<inline-formula><mml:math id="M567" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from this fen during snowmelt are
correlated with air temperature and thus with daily snowmelt and release of
trapped gases (Jammet et al., 2015), as seen elsewhere (Friborg et al., 1997;
Gažovič et al., 2010). The flux rates during the thaw season were
however much lower than during the summer. On the other hand, both CH<inline-formula><mml:math id="M568" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
and CO<inline-formula><mml:math id="M569" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from the lake peaked during the spring season. These
pulses coincided with the time of complete water overturn following ice-out
on the lake (Fig. 2) and can be explained by the release of gases previously
stored in and under lake ice. The annual seasonality was measured from
2.5 years of measurements, and further years of observations are needed to
evaluate and explain inter-annual variability in the magnitude of the
emissions.</p>
      <p id="d1e7292">The mean annual CH<inline-formula><mml:math id="M570" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> efflux from the lake is in line with a regional
estimate of ebullition flux in post-glacial and glacial lakes
(32.2 mg CH<inline-formula><mml:math id="M571" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M572" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> d<inline-formula><mml:math id="M573" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>; Wik et al., 2016). Mean fen CH<inline-formula><mml:math id="M574" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
fluxes agreed well with chamber measurements conducted over the same period
in <italic>Eriophorum</italic>-dominated plots in the Stordalen Mire (P. Crill,
unpublished data). The mean CH<inline-formula><mml:math id="M575" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux measured during the ice-free
seasons is in the upper range of summer CH<inline-formula><mml:math id="M576" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes measured in northern
wetlands that are dominated by sedges (ca. 40 to
280 mg CH<inline-formula><mml:math id="M577" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M578" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> d<inline-formula><mml:math id="M579" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, 25th–95th percentiles, Olefeldt et
al., 2013). Measured CO<inline-formula><mml:math id="M580" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux rates at the fen site also agreed with
previous EC studies within the wettest part of the mire (e.g., Christensen et
al., 2012) and with flux rates measured with gas chambers in sedge-dominated
vegetation plots in previous years (Bäckstrand et al., 2010) and during
the study period (P. Crill, unpublished data), at the seasonal and annual
scales. The fen is thus representative of minerotrophic northern fens where
high CH<inline-formula><mml:math id="M581" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions are measured due to year-round anoxia in the soil and
due to the dominance of vascular plants (Olefeldt et al., 2013). Lakes that
freeze solid in winter are not expected to emit a significant amount of
CO<inline-formula><mml:math id="M582" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> at the surface, unless ice-free holes caused by strong bubble seeps
are present (e.g., Sepulveda-Jauregui et al., 2015), which we do not observe
in the lakes of Stordalen (Wik et al., 2011). The observation of CO<inline-formula><mml:math id="M583" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fluxes from the lake during the second winter at rates that are within the
magnitude of land winter respiration (Fig. 3) was thus unexpected. The high
winter flux rates were coincident with strong winds, increasing air
temperature, and high latent heat flux. Whether these are due to a physical
evasion of CO<inline-formula><mml:math id="M584" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> through snow over the lake surface or due to lateral
advection of land-emitted CO<inline-formula><mml:math id="M585" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> is unclear. Increased ambient CO<inline-formula><mml:math id="M586" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
concentration over the lake in winter may be an indication of non-turbulent
transport of CO<inline-formula><mml:math id="M587" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> from land. Indeed, the extended flux footprint in
winter might include part of the land in the middle of the lake, leading to
vegetation-like flux magnitudes. Although this effect was limited by
filtering for large wind dispersion during winter periods, part of the flux
could still be influenced by land respiration to an extent that we cannot
quantify.</p>
      <p id="d1e7475">During the summer, the low magnitude of CO<inline-formula><mml:math id="M588" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes from the lake
resulted in a low signal-to-noise ratio (high relative random error). The
uncertainty linked to the inclusion of low-frequency contributions is a
problem that has been discussed widely in the eddy covariance community,
particularly for low-flux environments (e.g., Sievers et al., 2015). Testing
CO<inline-formula><mml:math id="M589" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux calculation with a new method that removes the low-frequency
contributions (Sievers et al., 2015) on a portion of our data in July 2012
showed nevertheless that the summer fluxes at the lake were coincident with
our measurement, with a negative mean and diel pattern with slight uptake
during the day (J. Sievers, personal communication, 2016). This indicates
that despite a high noise our CO<inline-formula><mml:math id="M590" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> lake flux measurements during summer
are trustworthy. In addition, the flux footprint was representative of each
ecosystem (lake vs. fen). The diel patterns of sensible and latent heat
fluxes from the lake resembled those observed in boreal lakes (Mammarella et
al., 2015; Nordbo et al., 2011; Shao et al., 2015; Vesala et al., 2006),
which further supports our EC measurement from the eastern sector being
representative of the lake surface. Overall, CO<inline-formula><mml:math id="M591" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes in the context
of a low-flux environment such as this lake should be interpreted with care;
we provide here the best estimate possible with the available instrumentation
at the time of the study.</p>
</sec>
<sec id="Ch1.S4.SS2">
  <?xmltex \opttitle{Season-dependent transport pathways of CH${}_{{4}}$ and
CO${}_{{2}}$ from the lake to the atmosphere}?><title>Season-dependent transport pathways of CH<inline-formula><mml:math id="M592" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M593" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> from the lake to the atmosphere</title>
<sec id="Ch1.S4.SS2.SSS1">
  <title>Ice-free season</title>
      <p id="d1e7544">Eddy covariance measures a direct flux across the surface–atmosphere
interface, spatially integrating over m<inline-formula><mml:math id="M594" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> to km<inline-formula><mml:math id="M595" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> all emitting
pathways that are responsible for the transport of gas from the ecosystem to
the atmosphere (i.e., total flux). In this study, CH<inline-formula><mml:math id="M596" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from the
lake during the ice-free seasons were dominated by short, large degassing
events (Figs. 3, C1) that coincided with drops in atmospheric pressure.
Furthermore, daily EC observations coincided with spatially averaged
ebullition fluxes measured with bubble traps (Fig. 6), which supports
CH<inline-formula><mml:math id="M597" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes being representative of the lake surface. These observations
also suggest that the total CH<inline-formula><mml:math id="M598" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> efflux from the lake during the ice-free
seasons was mostly due to the release of bubbles formed in the sediments
(ebullition), in line with previous observations that ebullition is the main
pathway for CH<inline-formula><mml:math id="M599" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions in shallow lake areas (Bastviken et al.,
2004).</p>
      <p id="d1e7602">A strong relationship was found between CH<inline-formula><mml:math id="M600" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> efflux and surface sediment
temperature; thus, the slight seasonality in summer CH<inline-formula><mml:math id="M601" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from
the lake (Fig. 5) is likely due to the seasonal increase in temperature in
the production zone. This seasonal trend also supports a bubble release
mechanism, since a seasonal increase in sediment temperature favors
methanogenesis and additionally causes a decrease in CH<inline-formula><mml:math id="M602" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> solubility
(Casper et al., 2000; Wik et al., 2013). This suggests that the amount of
CH<inline-formula><mml:math id="M603" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emitted at the lake surface is directly linked to the amount of
CH<inline-formula><mml:math id="M604" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> produced within the sediments, as has been observed using bubble
traps (Wik et al., 2014). A significant relationship between bubble flux and
surface sediment temperature similar to the one we reported here was observed
in the lakes of the Stordalen catchment by Wik et al. (2014), who identified
the threshold for ebullition in the Stordalen lakes at 6 <inline-formula><mml:math id="M605" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. Our EC
system measures fluxes for sediment temperatures under 6 <inline-formula><mml:math id="M606" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, which
could be diffusive. The occasional occurrence of degassing during summer that
timed up with short de-stratification events (Fig. S3 in the Supplement)
indicates that hydrodynamic transport and diffusion of CH<inline-formula><mml:math id="M607" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> linked to
lake mixing may happen in this lake, as has been observed in a boreal lake
(Podgrajsek et al., 2014). Water currents can also trigger bubble release by
disturbing surface sediments (Joyce and Jewell, 2003).</p>
      <p id="d1e7678">Exchange of CO<inline-formula><mml:math id="M608" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> across the lake–air interface is mainly
diffusion-limited due to the temperature of dissolution of CO<inline-formula><mml:math id="M609" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in water,
which does not favor the release of CO<inline-formula><mml:math id="M610" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in bubbles (Tranvik et al.,
2009). On average, the net CO<inline-formula><mml:math id="M611" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux at the surface of the lake during
the ice-free seasons revealed photosynthetic activity. The strong light
response curve of median diel emissions (Fig. 9) is largely influenced by
flux rates measured during the warm, sunny summer of 2014. The presence of
the diel pattern in summertime CO<inline-formula><mml:math id="M612" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes was tested for the influence
of advection from the lake shore by recalculating the fluxes from the lake
using a 5 min average instead of 30 min (Eugster, 2003; Podgrajsek et al.,
2015; Vesala et al., 2006). The pattern persisted for 5 min averaged fluxes
during the summer of 2012 (Fig. S5 in the Supplement), which suggests that
advection had a small effect on the summer CO<inline-formula><mml:math id="M613" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes.</p>
      <p id="d1e7736">CO<inline-formula><mml:math id="M614" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake at the lake in summer was associated with unstable
atmospheric conditions and positive H (Table 2). Waterside convection due to
cooling of the lake surface has been shown to enhance the diffusion-limited
exchange of CO<inline-formula><mml:math id="M615" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (Eugster, 2003; Podgrajsek et al., 2015). If the lake
water is under-saturated in CO<inline-formula><mml:math id="M616" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> with respect to the atmosphere, this
results in a downward CO<inline-formula><mml:math id="M617" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux. The anti-correlation we observe between
CO<inline-formula><mml:math id="M618" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux and H during summer could thus be due to the diffusive CO<inline-formula><mml:math id="M619" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
flux between the surface and the atmosphere being enhanced by convection near
the lake surface. Diel patterns in CO<inline-formula><mml:math id="M620" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux linked to lake mixing have
been observed in other eddy covariance studies, where they are associated
with a release of CO<inline-formula><mml:math id="M621" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> into the atmosphere (Mammarella et al., 2015;
Podgrajsek et al., 2015).</p>
      <p id="d1e7813">Finally, the low burst of CO<inline-formula><mml:math id="M622" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> observed in fall 2014 may be the result of
an accumulation of CO<inline-formula><mml:math id="M623" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> during the warmer summer 2014, when sustained
warm temperatures could cause a thermal stratification of the lake at the end
of the season. When lake cooling in fall triggers water mixing, accumulated
gases at the lake bottom can be released to the atmosphere (e.g., Kankaala et
al., 2006). In other years, regular mixing of the lake during summer may have
prevented this phenomenon from occurring.</p>
</sec>
<sec id="Ch1.S4.SS2.SSS2">
  <title>Thaw season</title>
      <p id="d1e7840">The strong correlation of CH<inline-formula><mml:math id="M624" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M625" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions at the lake during
both spring periods suggests that the gases were emitted into the atmosphere
via the same mechanism, i.e., by turbulence-driven release of gases that have
been accumulating in the lake. Conversely, the correlation is very low during
the ice-free periods, when ebullition is the dominant process of CH<inline-formula><mml:math id="M626" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
release. The outgassing pattern at thaw coincided in both years with the
breakdown of thermal stratification in the water column after complete ice
disappearance. Bubbles trapped in the winter ice of lake Villasjön
contain both CH<inline-formula><mml:math id="M627" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M628" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (Boereboom et al., 2012). CO<inline-formula><mml:math id="M629" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> stored
in lake ice during winter can originate from benthic respiration which can
occur under ice while dead plants from the previous summer are decomposing
(Karlsson et al., 2008). Methanotrophy can be important during overturn
events in lakes (Kankaala et al., 2006; Schubert et al., 2012); thus,
CO<inline-formula><mml:math id="M630" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> may also be produced in lake water during ice thaw, which lasts
several days, as an output of CH<inline-formula><mml:math id="M631" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> oxidation. Dissolved CO<inline-formula><mml:math id="M632" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> could
also enter the lake as catchment input via lateral meltwater run-off before
complete overturn (Denfeld et al., 2015).</p>
      <p id="d1e7925">The processes underlying CH<inline-formula><mml:math id="M633" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> degassing during thaw in 2013 have been
discussed in detail in a previous study (Jammet et al., 2015), suggesting
that the spring burst is the combination of different gas sources, i.e.,
liberation of bubbles from the ice, diffusion of gases from the water to the
air, and release of stored gases from the bottom of the lake during complete
overturn. As CO<inline-formula><mml:math id="M634" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes covariate closely with CH<inline-formula><mml:math id="M635" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from
the lake during spring (Fig. S4 in the Supplement), it is likely that
CO<inline-formula><mml:math id="M636" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> was released via the same physical mechanisms. The degassing pattern
observed in 2013 was repeated in 2014, with a mean and median CH<inline-formula><mml:math id="M637" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux
rate smaller than the previous year but still significantly higher than the
CH<inline-formula><mml:math id="M638" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions of the ice-free season (Fig. S2 in the Supplement). In
2014 the thaw period started earlier but was longer (Fig. 2), and our
measurement system may have missed part of the degassing due to instrument
failure. As ice thaws, gases contained in bubbles can migrate to the water
(Greene et al., 2014) and be released into the atmosphere when thermal
stratification gradually breaks because of the warming up of the water
column. We can speculate that a delay in the timing of overturn following ice
thaw may favor oxidation of CH<inline-formula><mml:math id="M639" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> within the water column when it is
already partly mixing, which would raise the concentration of dissolved
CO<inline-formula><mml:math id="M640" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in the water and could contribute to a smaller burst of CH<inline-formula><mml:math id="M641" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
during complete overturn.</p>
</sec>
</sec>
<sec id="Ch1.S4.SS3">
  <title>Annual atmospheric carbon budget</title>
<sec id="Ch1.S4.SS3.SSS1">
  <title>Carbon function</title>
      <p id="d1e8022">The fen was an annual sink of carbon with respect to the atmosphere, while
the lake was an annual source, at a magnitude representing 70 % of the
fen sink. The total annual C-emission from the lake is within the range of
annual C-emissions (CH<inline-formula><mml:math id="M642" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> <inline-formula><mml:math id="M643" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> CO<inline-formula><mml:math id="M644" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) from lakes of subarctic Sweden
(5 to 54 g C m<inline-formula><mml:math id="M645" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M646" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, Lundin et al., 2015) estimated mostly
using water grab sampling.</p>
      <p id="d1e8074">At the fen, we report a stronger summer sink of CO<inline-formula><mml:math id="M647" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (three ice-free
seasons average <inline-formula><mml:math id="M648" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>206.8 g C m<inline-formula><mml:math id="M649" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, Table 3) compared to earlier
studies in the inner fens of the Stordalen mire (<inline-formula><mml:math id="M650" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>133 g C m<inline-formula><mml:math id="M651" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>,
years 2001–2008, Christensen et al., 2012), but annually a net CO<inline-formula><mml:math id="M652" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
uptake (<inline-formula><mml:math id="M653" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>58.5 to <inline-formula><mml:math id="M654" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>79.1, average <inline-formula><mml:math id="M655" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>66.3 g C m<inline-formula><mml:math id="M656" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M657" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) that
is similar to the 2001–2008 average
(<inline-formula><mml:math id="M658" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>66 g C–CO<inline-formula><mml:math id="M659" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M660" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M661" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, Christensen et al., 2012) and
smaller than the average for years 2006–2008, which were warm years
(<inline-formula><mml:math id="M662" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>90 g C–CO<inline-formula><mml:math id="M663" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M664" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M665" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, Christensen et al., 2012). The
difference is due to the higher CO<inline-formula><mml:math id="M666" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> respiration we measured in winter,
which equaled 54 % of the summer sink on average during the measuring
period. The annual CH<inline-formula><mml:math id="M667" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions of
21.2 C–CH<inline-formula><mml:math id="M668" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> m<inline-formula><mml:math id="M669" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M670" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Table 3) are very close to what has
been reported for the internal fens of Stordalen in an eddy covariance study
where winter emissions were estimated with a temperature relationship
(Jackowicz-Korczyński et al., 2010). This highlights the stability of the
fen in terms of CH<inline-formula><mml:math id="M671" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions, but also the low sensitivity of the
annual sum to the choice of gap filling method for the fen CH<inline-formula><mml:math id="M672" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> flux
dataset, which is tightly linked to temperature.</p>
      <p id="d1e8331">To determine whether an ecosystem is a net source or sink of carbon within
the landscape carbon cycling, a full net ecosystem carbon balance (NECB) must
take into account not only vertical carbon exchange, but also lateral carbon
transport, in and out of the system (Chapin et al., 2006). In 2008, net DOC
export at the fen was 8.1 g C m<inline-formula><mml:math id="M673" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M674" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and net POC export was
0.6 g C m<inline-formula><mml:math id="M675" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M676" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Olefeldt and Roulet, 2012). Combined with our
annual atmospheric carbon budget (Table 3), this results in a fen NECB of
<inline-formula><mml:math id="M677" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>29.5 g C m<inline-formula><mml:math id="M678" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M679" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the first year and
<inline-formula><mml:math id="M680" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>43.3 g C m<inline-formula><mml:math id="M681" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M682" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the second year. These numbers are
marginally smaller than the long-term carbon accumulation of
<inline-formula><mml:math id="M683" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>51 g C m<inline-formula><mml:math id="M684" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M685" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> inferred from the analysis of a peat cored
in Stordalen and attributed to a period when the mire was dominated by
graminoids (Kokfelt et al., 2010). We are not aware of existing data on net
export of DOC and POC through the lake to make a similar estimate.</p>
      <p id="d1e8477">In terms of radiative forcing, considering the 28-fold stronger global
warming potential of atmospheric CH<inline-formula><mml:math id="M686" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> vs. atmospheric CO<inline-formula><mml:math id="M687" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> over
100 years (GWP100, Myhre et al., 2013), vertical carbon exchange has a
warming impact on the atmosphere at both ecosystems through their net annual
emissions of CH<inline-formula><mml:math id="M688" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>. Annual estimates that disregard winter and
transitional seasons are likely missing part of the annual carbon emissions
from seasonally freezing lakes and wetlands.</p>
</sec>
<sec id="Ch1.S4.SS3.SSS2">
  <?xmltex \opttitle{The lake as a summer CO${}_{{2}}$ sink}?><title>The lake as a summer CO<inline-formula><mml:math id="M689" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sink</title>
      <p id="d1e8523">Because of dynamic external and internal factors governing the consumption
and production of CO<inline-formula><mml:math id="M690" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in surface waters, the CO<inline-formula><mml:math id="M691" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> function of a lake
can vary seasonally (Maberly, 1996; Shao et al., 2015). Lake Villasjön
was an annual source of CO<inline-formula><mml:math id="M692" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> due to the spring outgassing, but it was a
small sink of CO<inline-formula><mml:math id="M693" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in the open-water period. While flux rates in summers
2012 and 2013 were negative but close to the noise level, the uptake was
larger and significant in 2014 when the summer was hotter and sunnier.
Averaged estimates from water sampling measurements in the lakes of the
Abisko area indicate the lakes to be mainly CO<inline-formula><mml:math id="M694" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sources during the
summer, except for a few lakes that were seasonal CO<inline-formula><mml:math id="M695" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sinks during the
ice-free season (Karlsson et al., 2013). In the few eddy covariance studies
available from Arctic and boreal sites, lakes are reported as CO<inline-formula><mml:math id="M696" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
sources during the ice-free season (Lohila et al., 2015; Mammarella et al.,
2015; Podgrajsek et al., 2015) and occasional CO<inline-formula><mml:math id="M697" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sinks during the warm
summer months, while being sources on the seasonal scale (Anderson et al.,
1999; Eugster, 2003; Huotari et al., 2011; Jonsson et al., 2008). No
coincident measurement of pCO<inline-formula><mml:math id="M698" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in the lake water is available for the
study period. A future study combining pCO<inline-formula><mml:math id="M699" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> with EC will help further
define the direction of the flux observed on the ecosystem scale.</p>
      <p id="d1e8617">Although Villasjön is representative of a widespread post-glacial lake
type across subarctic and Arctic latitudes, it differs from most lakes
studied in the northern lakes literature due to its particularly shallow
depth, which results in the lack of long-term stratification during the
open-water season. Lakes that are similarly shallow are often thermokarst
lakes or peatland ponds (Vonk et al., 2015). Summer CO<inline-formula><mml:math id="M700" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake at the
level of what we report here has been observed in highly productive lakes
(Pacheco et al., 2013) or in thaw ponds colonized by submerged plants and
microbial mats (Laurion et al., 2010; Tank et al., 2009). Estimates of
air–lake carbon exchange using water sampling and floating chambers
(Karlsson et al., 2013) showed that a minority of lakes in subarctic Sweden
were CO<inline-formula><mml:math id="M701" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sinks in summer, with a total seasonal CO<inline-formula><mml:math id="M702" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange from
<inline-formula><mml:math id="M703" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>3.8 to <inline-formula><mml:math id="M704" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>10 g C m<inline-formula><mml:math id="M705" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> yr<inline-formula><mml:math id="M706" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, while being large sources at
ice-out, offsetting the summer sink.</p>
      <p id="d1e8686">Lakes with poor hydrological connections with their upstream catchment have
been reported in previous studies to be net CO<inline-formula><mml:math id="M707" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sinks in summer, e.g.,
in Minnesota (Striegl and Michmerhuizen, 1998) or in thaw ponds of the
Canadian Arctic (Tank et al., 2009). In the latter study, within-lake DOC was
proposed to occur as a byproduct of macrophyte photosynthesis, showing that
net CO<inline-formula><mml:math id="M708" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake in lakes is not always associated with low DOC
concentrations. In large and shallow lakes surrounded by peatlands,
vegetation develops on the sediment surface thanks to the presence of humic
acids supplied by the peaty shores and a well-illuminated bottom (Banaś
et al., 2012). The analysis of peat and lake sediment records in Stordalen
suggested that a significant amount of peat is exported from the mire to lake
Villasjön during periods of mire erosion, likely due to permafrost thaw
(Kokfelt et al., 2010). This lake may have high nutrient content due to peat
input at the shores, organic-rich sediments, and autochthonous vegetation.
Lakes that do not stratify tend to be more productive because of the more
regular mixing of nutrients (Tranvik et al., 2009; Wetzel, 2001).</p>
</sec>
<sec id="Ch1.S4.SS3.SSS3">
  <title>Influence of overturn on annual C-emissions</title>
      <p id="d1e8713">On an annual scale, the thaw period accounted for 50 % of annual carbon
exchange (CH<inline-formula><mml:math id="M709" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> <inline-formula><mml:math id="M710" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> CO<inline-formula><mml:math id="M711" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) at lake Villasjön and turned the lake
from a summer CO<inline-formula><mml:math id="M712" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sink into an annual source. In other, deeper lakes
that stratify in summer and do not fully mix in spring, fall overturn led to
the highest emissions of CH<inline-formula><mml:math id="M713" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> or CO<inline-formula><mml:math id="M714" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> of the year (Kankaala et al.,
2006; Schubert et al., 2012), accounting for a large part of the annual
CO<inline-formula><mml:math id="M715" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux (Huotari et al., 2011). Other seasonally ice-covered lakes
emitted large amounts of CH<inline-formula><mml:math id="M716" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M717" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> following ice-out (Anderson et
al., 1999; Karlsson et al., 2013), while high concentrations of dissolved
CO<inline-formula><mml:math id="M718" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M719" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> under lake ice have been measured in North American
lakes (Striegl and Michmerhuizen, 1998), across lakes of the Swedish
subarctic (Karlsson et al., 2013), in Alaskan thermokarst lakes
(Sepulveda-Jauregui et al., 2015), or in thaw ponds in Canada (Tank et al.,
2009). Accumulation of CH<inline-formula><mml:math id="M720" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M721" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> under the ice is thus a general
feature of lakes with an anoxic hypolimnion or sediment in winter, but
studies reporting direct measurement of the outgassing of CH<inline-formula><mml:math id="M722" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M723" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> at the lake surface right after thaw are scarce because it is a
rapid and variable phenomenon that is seldom included in direct flux
measurements.</p>
      <p id="d1e8851">The large impact of CO<inline-formula><mml:math id="M724" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M725" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> release during spring has been
observed in lakes of the Abisko area where water samples before and after
ice-out were used to estimate the thaw release, which accounted on average
for 45 % of annual emissions (Karlsson et al., 2013; Lundin et al.,
2013). A few regional studies reported on a lesser importance of the spring
season for annual carbon emissions from lakes. Sepulveda-Jauregui et
al. (2015) sampled 40 Alaskan thermokarst lakes where the maximum emissions
of CH<inline-formula><mml:math id="M726" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M727" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> were measured in summer. Many of these lakes were
thermokarst lakes that continuously emitted CH<inline-formula><mml:math id="M728" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> in winter through open
holes, which we do not observe in lake Villasjön. Thermokarst lakes are
usually stronger CH<inline-formula><mml:math id="M729" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emitters than post-glacial lakes on a per unit area
basis, yet post-glacial lakes seem to be a larger overall source because they
cover a larger area at the high northern latitudes (Wik et al., 2016). A
recent review by Wik et al. (2016) compiled CH<inline-formula><mml:math id="M730" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions from several
types of lakes. Over the total of 733 sites, the thaw period was estimated to
contribute <inline-formula><mml:math id="M731" display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 23 % of annual emissions of lakes and ponds. Only four
sites were measured with EC, and those four only comprised ice-free season
(July–August) measurements. Thus the comparison to our results is limited by
differences in the temporal and spatial scale of the methods.</p>
      <p id="d1e8925">Our study underlines the high significance of shoulder seasons (more
precisely, overturn periods following periods of gas storage) for the
biogeochemistry of lakes and the emission of CO<inline-formula><mml:math id="M732" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M733" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> into the
atmosphere. The relative importance of these periods for the annual emissions
depends on the extent of the overturn (Huotari et al., 2011; Kankaala et al.,
2006), the extent of methanotrophy during and before full lake mixing
(Kankaala et al., 2006; Schubert et al., 2012), as well as the amount of
degradable organic matter in the hypolimnion. Although these overturn periods
cover only a few weeks or days, they are important for both CH<inline-formula><mml:math id="M734" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and
CO<inline-formula><mml:math id="M735" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emissions in lakes and should be included in measurement campaigns
when feasible.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions</title>
      <p id="d1e8973">The waterlogged fen and the shallow lake showed contrasting annual cycles in
terms of CH<inline-formula><mml:math id="M736" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M737" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> exchange with the atmosphere. This difference
is explained, first, by the presence of an ice lid over the lake surface
which led to the storage of gases in winter and large subsequent emissions in
spring, while evasion of CH<inline-formula><mml:math id="M738" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M739" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> to the atmosphere from the fen
in the wintertime limits the importance of emissions during ice melt and
snowmelt. Second, the dense cover of vascular plants at the fen leads to high
CH<inline-formula><mml:math id="M740" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> emissions and CO<inline-formula><mml:math id="M741" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> uptake in summer.</p>
      <p id="d1e9031">Annually, the fen was a net carbon sink with respect to the atmosphere, while
the lake was a source of carbon due to the degassing in spring that
outweighed the apparent uptake of CO<inline-formula><mml:math id="M742" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in summer. This study confirms the
importance of overturn periods in lakes for both CH<inline-formula><mml:math id="M743" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> and CO<inline-formula><mml:math id="M744" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> annual
emissions. The magnitude of the degassing during the thaw season may depend
greatly on lake type, morphometry, and productivity status. The lake studied represents a common type
of shallow post-glacial lake across the subarctic latitudes. Further direct
measurements of surface fluxes covering several years and different lake
types are needed to evaluate the inter-annual variability in the magnitude of
the degassing in shoulder seasons as well as its importance for the annual
emissions of northern lakes in general.</p>
      <p id="d1e9061">Finally, ebullition was identified as the main transport pathway for CH<inline-formula><mml:math id="M745" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
emissions in the shallow subarctic lake, and a net CO<inline-formula><mml:math id="M746" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> sink in summer
indicated photosynthetic activity. Turbulence-driven diffusive release of
CO<inline-formula><mml:math id="M747" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and CH<inline-formula><mml:math id="M748" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> was predominant during spring overturn following
ice-out. These results show the potential of the EC method in lake
environments for a better understanding of flux processes and annual
seasonality in the understudied but abundant post-glacial lakes and ponds.</p>
</sec>

      
      </body>
    <back><notes notes-type="dataavailability">

      <p id="d1e9104">The eddy covariance data and meteorological data used in
this study are available upon request to the lead author. A version of the
flux dataset before flux source partitioning between lake and fen is
available with ancillary data on the FLUXNET data portal under  site code
name SE-St1 (<uri>http://fluxnet.fluxdata.org</uri>).</p>
  </notes><?xmltex \hack{\clearpage}?><app-group>

<app id="App1.Ch1.S1">
  <title>Details in eddy covariance flux calculation</title>
      <p id="d1e9119">Processing of the raw eddy covariance data for flux calculation included
despiking (Vickers and Mahrt, 1997), angle of attack correction on raw wind
components (Nakai et al., 2006), 2-D axis rotation (Wilczak et al., 2001) on
wind speed components, and detrending of 30 min raw data intervals by block
averaging the vertical wind speed and scalar signals (Moncrieff et al.,
2004). The time delay between vertical wind speed and gas concentration
measurements (CO<inline-formula><mml:math id="M749" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, CH<inline-formula><mml:math id="M750" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, H<inline-formula><mml:math id="M751" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O) was removed by finding the
maximum of the cross-covariance function of vertical wind speed and each
scalar (Fan et al., 1990). The time-window search was set to <inline-formula><mml:math id="M752" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 4 s for
CO<inline-formula><mml:math id="M753" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and H<inline-formula><mml:math id="M754" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O; the median time lag was 0 s. For CH<inline-formula><mml:math id="M755" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, the
time-window search was adjusted for each period when a change in the setup
occurred; the median time lag between vertical wind speed and CH<inline-formula><mml:math id="M756" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
concentration measurements varied between 9 and 18 s.</p>
      <p id="d1e9193">The effect of density fluctuations on CO<inline-formula><mml:math id="M757" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes was corrected (Webb et
al., 1980). The correction lowered the amplitude of the CO<inline-formula><mml:math id="M758" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux dataset
on average by 53% (slope of the linear regression between non-density
corrected CO<inline-formula><mml:math id="M759" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes and final corrected fluxes <inline-formula><mml:math id="M760" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.47,
<inline-formula><mml:math id="M761" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> = 0.73). Due to the unavailability of H<inline-formula><mml:math id="M762" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration
measurements from the methane analyzer during most of the study period, WPL
correction was not applied by the flux software on CH<inline-formula><mml:math id="M763" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes. Applying
the correction on part of the data using the available H<inline-formula><mml:math id="M764" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O concentration
from the methane analyzer showed a difference in flux magnitude of about
1 % with the non-corrected dataset. The low magnitude of the WPL
correction can be expected for this setup, due to the long sampling line that
attenuates significantly the H<inline-formula><mml:math id="M765" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>O signal as well as temperature and
pressure fluctuations, and thus density effects. Turbulent fluxes calculated
with the eddy covariance method are affected by spectral losses due to the
instrumental setup and the limited time response of the instruments. Losses
in the low-frequency range due to the finite flux averaging time were
corrected analytically after Moncrieff et al. (2004). CO<inline-formula><mml:math id="M766" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> flux loss in
the high-frequency range was also corrected analytically (Moncrieff et al.,
1997), while CH<inline-formula><mml:math id="M767" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes derived from the closed-path system required an
in situ assessment of the system's cut-off frequency (Ibrom et al., 2007)
due to the long sampling line. This assessment was done separately for each
period with a continuous instrumental setup and the associated flux
attenuation was calculated and compensated following the formulation by
Horst (1997). The magnitude of the spectral loss and hence of the total
spectral correction was on average 31 % for CO<inline-formula><mml:math id="M768" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes and 37 %
for CH<inline-formula><mml:math id="M769" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes.</p><?xmltex \hack{\clearpage}?>
</app>

<app id="App1.Ch1.S2">
  <title>Computing the performance of the ANN models</title>
      <p id="d1e9322">The performance of the ANN models was assessed by comparing the predicted
values with original observed values of the entire dataset (Table B1). This
represents the actual ability of the ANN to generalize (Papale and Valentini
2003) to untrained conditions. The goodness of fit was quantified with the
coefficient of determination <inline-formula><mml:math id="M770" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> and the root mean square error (RMSE).
Additionally, the mean random error of the predicted flux values was
calculated as the mean of the standard deviation around each individual value
used for gap filling. In other words: each modeled value used for gap filling
is the mean of several ANN model runs. The 25 best runs (according to
<inline-formula><mml:math id="M771" display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula>) were averaged to obtain the modeled fluxes used in the gap filling.
The standard deviation of these 25 model outputs was thus used as a
quantification of the random error of each modeled flux value. The average of
these individual random errors was then computed as the mean random error of
each modeled flux series (CH<inline-formula><mml:math id="M772" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fen, CH<inline-formula><mml:math id="M773" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> lake, CO<inline-formula><mml:math id="M774" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fen) reported
in Table B1.</p>

<?xmltex \floatpos{t}?><table-wrap id="App1.Ch1.T1" specific-use="star"><caption><p id="d1e9377">Characteristics of the artificial neural networks that were
developed for gap filling fen and lake CH<inline-formula><mml:math id="M775" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> fluxes and fen CO<inline-formula><mml:math id="M776" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fluxes. All networks were developed with one hidden layer and with four fuzzy
datasets as additional input to force seasonality. The mean random error is
the average of the standard deviation around the modeled flux values for each
series (cf. Text S1 in the Supplement).</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Fen CH<inline-formula><mml:math id="M777" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">Fen CO<inline-formula><mml:math id="M778" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">Lake CH<inline-formula><mml:math id="M779" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Input variables</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math id="M780" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">air</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">Photosynthetic active</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M781" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">air</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">radiation (PAR)</oasis:entry>  
         <oasis:entry colname="col4"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"><inline-formula><mml:math id="M782" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">peat</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> at 10 cm</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math id="M783" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">air</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M784" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> water at  10 cm</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Wind speed</oasis:entry>  
         <oasis:entry colname="col3">Vapour pressure</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M785" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> in sediment surface  (100 cm)</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">deficit</oasis:entry>  
         <oasis:entry colname="col4"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Air pressure</oasis:entry>  
         <oasis:entry colname="col3">(VPD)</oasis:entry>  
         <oasis:entry colname="col4">Wind speed</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Net radiation (fen)</oasis:entry>  
         <oasis:entry colname="col3">Net radiation (fen)</oasis:entry>  
         <oasis:entry colname="col4">Air  pressure</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Incoming solar radiation</oasis:entry>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">Net radiation  (lake)</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">Incoming solar radiation</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Number of neurons</oasis:entry>  
         <oasis:entry colname="col2">6</oasis:entry>  
         <oasis:entry colname="col3">6</oasis:entry>  
         <oasis:entry colname="col4">9</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">R2 (all predicted vs. obs.)</oasis:entry>  
         <oasis:entry colname="col2">0.85</oasis:entry>  
         <oasis:entry colname="col3">0.86</oasis:entry>  
         <oasis:entry colname="col4">0.70</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">RMSE (all predicted vs.</oasis:entry>  
         <oasis:entry colname="col2">0.022</oasis:entry>  
         <oasis:entry colname="col3">1.25</oasis:entry>  
         <oasis:entry colname="col4">0.043</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">obs., <inline-formula><mml:math id="M786" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M787" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M788" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Mean random error of all predicted</oasis:entry>  
         <oasis:entry colname="col2">0.004</oasis:entry>  
         <oasis:entry colname="col3">1.3</oasis:entry>  
         <oasis:entry colname="col4">0.011</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">values (<inline-formula><mml:math id="M789" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M790" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M791" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

<?xmltex \hack{\clearpage}?>
</app>

<app id="App1.Ch1.S3">
  <title/>

      <?xmltex \floatpos{h!}?><fig id="App1.Ch1.F1"><caption><p id="d1e9782">Probability density functions of <bold>(a)</bold> the measured CH<inline-formula><mml:math id="M792" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>
fluxes (bin size 10 nmol m<inline-formula><mml:math id="M793" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M794" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) and <bold>(b)</bold> the measured
CO<inline-formula><mml:math id="M795" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes (bin size 0.2 <inline-formula><mml:math id="M796" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math id="M797" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M798" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) from the
fen and from the lake during the entire measurement period.</p></caption>
        <?xmltex \hack{\hsize\textwidth}?>
        <?xmltex \igopts{width=284.527559pt}?><graphic xlink:href="https://bg.copernicus.org/articles/14/5189/2017/bg-14-5189-2017-f11.png"/>

      </fig>

<?xmltex \hack{\clearpage}?><supplementary-material position="anchor"><p id="d1e9874"><bold>The Supplement related to this article is available online at <inline-supplementary-material xlink:href="https://doi.org/10.5194/bg-14-5189-2017-supplement" xlink:title="pdf">https://doi.org/10.5194/bg-14-5189-2017-supplement</inline-supplementary-material>.</bold></p></supplementary-material>
</app>
  </app-group><notes notes-type="authorcontribution">

      <p id="d1e9882">TF, MJ, and PC designed the study. MJ collected, analyzed, and
interpreted the data. SD developed and performed the gap filling modeling. EK
pre-processed part of the eddy covariance raw data. FJWP performed the 2-D
footprint modeling and drew the footprint figure. MW provided methane
ebullition data. MJ wrote the manuscript and figures and all authors
commented on them.</p>
  </notes><notes notes-type="competinginterests">

      <p id="d1e9888">The authors declare that they have no conflict of
interest.</p>
  </notes><notes notes-type="sistatement">

      <p id="d1e9894">This article is part of the special issue “Interactions between
climate change and the Cryosphere: SVALI, DEFROST, CRAICC (2012–2016)
(TC/ACP/BG inter-journal SI)”. It is not associated with a conference.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e9900">This work was funded through the Nordic Centre of Excellence, DEFROST, under
the Nordic Top-Level Research Initiative, and collaborative research project
Changing Permafrost in the Arctic and its Global Effects in the 21st century
(PAGE21). We thank the EU-funded International Network for Terrestrial
Research and Monitoring in the Arctic (INTERACT) for financing visits at the
field station, the Danish National Research Foundation for supporting
activities within the Center of Permafrost (CENPERM, DNRF100), and the Abisko
Scientific Research Station for providing field work infrastructure. We thank
Tyler Logan, Fabian Rey, Robert Holden, Niklas Rakos, and Mathias Madsen for
technical assistance and maintenance in the field.<?xmltex \hack{\\\\}?>Edited by:
Steffen M. Noe <?xmltex \hack{\\}?>Reviewed by: Ivan Mammarella, Christian Wille,
<?xmltex \hack{\newline}?>and one anonymous referee</p></ack><ref-list>
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    <!--<article-title-html>Year-round CH<sub>4</sub> and CO<sub>2</sub> flux dynamics in two contrasting freshwater ecosystems of the subarctic</article-title-html>
<abstract-html><p class="p">Lakes and wetlands, common ecosystems of the high northern
latitudes, exchange large amounts of the climate-forcing gases methane
(CH<sub>4</sub>) and carbon dioxide (CO<sub>2</sub>) with the atmosphere. The magnitudes
of these fluxes and the processes driving them are still uncertain,
particularly for subarctic and Arctic lakes where direct measurements of
CH<sub>4</sub> and CO<sub>2</sub> emissions are often of low temporal resolution and are
rarely sustained throughout the entire year.</p><p class="p">Using the eddy covariance method, we measured surface–atmosphere exchange of
CH<sub>4</sub> and CO<sub>2</sub> during 2.5 years in a thawed fen and a shallow lake of
a subarctic peatland complex. Gas exchange at the fen exhibited the expected
seasonality of a subarctic wetland with maximum CH<sub>4</sub> emissions and
CO<sub>2</sub> uptake in summer, as well as low but continuous emissions of
CH<sub>4</sub> and CO<sub>2</sub> throughout the snow-covered winter. The seasonality of
lake fluxes differed, with maximum CO<sub>2</sub> and CH<sub>4</sub> flux rates recorded
at spring thaw. During the ice-free seasons, we could identify surface
CH<sub>4</sub> emissions as mostly ebullition events with a seasonal trend in the
magnitude of the release, while a net CO<sub>2</sub> flux indicated photosynthetic
activity. We found correlations between surface CH<sub>4</sub> emissions and
surface sediment temperature, as well as between diel CO<sub>2</sub> uptake and
diel solar input. During spring, the breakdown of thermal stratification
following ice thaw triggered the degassing of both CH<sub>4</sub> and CO<sub>2</sub>.
This spring burst was observed in 2 consecutive years for both gases, with a
large inter-annual variability in the magnitude of the CH<sub>4</sub> degassing.</p><p class="p">On the annual scale, spring emissions converted the lake from a small
CO<sub>2</sub> sink to a CO<sub>2</sub> source: 80 % of total annual carbon emissions
from the lake were emitted as CO<sub>2</sub>. The annual total carbon exchange per
unit area was highest at the fen, which was an annual sink of carbon with
respect to the atmosphere. Continuous respiration during the winter partly
counteracted the fen summer sink by accounting for, as both CH<sub>4</sub> and
CO<sub>2</sub>, 33 % of annual carbon exchange. Our study shows (1) the
importance of overturn periods (spring or fall) for the annual CH<sub>4</sub> and
CO<sub>2</sub> emissions of northern lakes, (2) the significance of lakes as
atmospheric carbon sources in subarctic landscapes while fens can be a strong
carbon sink, and (3) the potential for ecosystem-scale eddy covariance
measurements to improve the understanding of short-term processes driving
lake–atmosphere exchange of CH<sub>4</sub> and CO<sub>2</sub>.</p></abstract-html>
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