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<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?>
  <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-13-4843-2016</article-id><title-group><article-title>Coccolithophore responses to environmental variability in the South China
Sea: species composition and calcite content</article-title>
      </title-group><?xmltex \runningtitle{Coccolithophore responses to environmental variability}?><?xmltex \runningauthor{X.~Jin et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Jin</surname><given-names>Xiaobo</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-8934-0348</ext-link></contrib>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Liu</surname><given-names>Chuanlian</given-names></name>
          <email>liucl@tongji.edu.cn</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Poulton</surname><given-names>Alex J.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-5149-6961</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Dai</surname><given-names>Minhan</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-0550-0701</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Guo</surname><given-names>Xianghui</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>State Key Laboratory of Marine Geology, Tongji University, 200092 Shanghai, China</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Ocean Biogeochemistry and Ecosystems, National Oceanography Centre,
Southampton, SO14 3ZH,  UK</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>State Key Laboratory of Marine Environmental Science, Xiamen
University, 361005 Xiamen, China</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Chuanlian Liu (liucl@tongji.edu.cn)</corresp></author-notes><pub-date><day>29</day><month>August</month><year>2016</year></pub-date>
      
      <volume>13</volume>
      <issue>16</issue>
      <fpage>4843</fpage><lpage>4861</lpage>
      <history>
        <date date-type="received"><day>5</day><month>March</month><year>2016</year></date>
           <date date-type="rev-request"><day>15</day><month>March</month><year>2016</year></date>
           <date date-type="rev-recd"><day>14</day><month>July</month><year>2016</year></date>
           <date date-type="accepted"><day>1</day><month>August</month><year>2016</year></date>
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016.html">This article is available from https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016.html</self-uri>
<self-uri xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016.pdf</self-uri>


      <abstract>
    <p>Coccolithophore contributions to the global marine carbon cycle are regulated
by the calcite content of their scales (coccoliths) and the relative cellular
levels of photosynthesis and calcification rates. All three of these factors
vary between coccolithophore species and with response to the growth
environment. Here, water samples were collected in the northern basin of the
South China Sea (SCS) during summer 2014 in order to examine how
environmental variability influenced species composition and cellular levels
of calcite content. Average coccolithophore abundance and their calcite
concentration in the water column were 11.82 cells mL<inline-formula><mml:math 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
1508.3 pg C mL<inline-formula><mml:math 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>, respectively, during the cruise. Water samples can
be divided into three floral groups according to their distinct
coccolithophore communities. The vertical structure of the coccolithophore
community in the water column was controlled by the trophic conditions, which
were regulated by mesoscale eddies across the SCS basin. The evaluation of
coccolithophore-based calcite in the surface ocean also showed that three key
species in the SCS (<italic>Emiliania huxleyi</italic>, <italic>Gephyrocapsa oceanica</italic>, <italic>Florisphaera profunda</italic>) and other larger, numerically rare
species made almost equal contributions to total coccolith-based calcite in
the water column. For <italic>Emiliania huxleyi</italic> biometry measurements,
coccolith size positively correlated with nutrients (nitrate, phosphate), and
it is suggested that coccolith length is influenced by light and nutrients
through the regulation of growth rates. Larger-sized coccoliths were also
linked statistically to low pH and calcite saturation states; however, it is
not a simple cause and effect relationship, as carbonate chemistry was
strongly co-correlated with the other key environmental factors (nutrients,
light).</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>Coccolithophores are an important component of marine phytoplankton
communities, contributing globally to both the organic carbon pump
(biological carbon pump) and the (calcium) carbonate (counter) pump.
Coccolithophores may contribute 10 to 20 % of total chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>,
and primary production and 30 to 60 % of calcium carbonate (calcite or
particulate inorganic carbon) in the water column in non-bloom conditions
(Poulton et al., 2006, 2007, 2010, 2014), although higher contributions of
organic carbon (&gt; 40 %) do occur in coccolithophore blooms
(Poulton et al., 2013). Coccolith-based calcite can contribute up to 80 %
to deep-sea carbonate fluxes (Sprengel et al., 2000, 2002; Young and Ziveri,
2000). High concentrations of the cosmopolitan coccolithophore species
<italic>Emiliania huxleyi</italic> can generate large quantities of cells and
detached coccoliths (e.g., <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2000 cells mL<inline-formula><mml:math 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
3 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula> coccoliths mL<inline-formula><mml:math 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>; Balch et al., 1991), which are
detectable from space (Cokacar et al., 2004; Raitsos et al., 2006); for
example, the Great Calcite Belt in the Southern Hemisphere is attributed
to high particulate inorganic carbon from coccolithophores (Balch et al.,
2011, 2014). To assess the contribution of coccolithophores to the carbon
cycle, two relevant issues are worthy of attention: (1) coccolithophore
species composition and calcite concentration in the water column and (2)
their calcification responses to oceanic environmental factors.</p>
      <p>The South China Sea (SCS) is the largest marginal sea in the west Pacific
Ocean, covering an area of 3.5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> km<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> (Wang et al.,
2014). Phytoplankton production and surface circulation in the northern basin
of the SCS are greatly influenced by the East Asian monsoon system. In the
northern part of SCS, during the summer season (June to August), the surface
water is oligotrophic and well stratified, and a stable mixed layer is
developed. The mean chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentration and primary production in
the euphotic zone is 0.08 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.03 mg m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
&lt; 30 mg C m<inline-formula><mml:math 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 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>, respectively (Chen, 2005; Chen et
al., 2006), with the nitricline at a depth of <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 60 m (Chen et al.,
2006). During the winter season (December to February), surface waters are
productive and well mixed due to the strong seasonal wind stress. Mean
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations and primary production are
0.65 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.17 mg m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and 550 mg C m<inline-formula><mml:math 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 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>,
respectively (Chen, 2005; Chen et al., 2006), with the nitricline much
shallower at around 5 to 20 m (Chen et al., 2006). Some preliminary work on
coccolithophore biogeography has been reported in the SCS (Okada and Honjo,
1975; Chen et al., 2007a; Sun et al., 2011); however, these studies are
confined to surface waters or sporadic sampling sites and lack any coccolith
weight estimation.</p>
      <p>Mesoscale eddies are typical physical oceanographic features in the SCS (Wang
et al., 2003) and significantly influence the structure of the upper
water column. Cyclonic eddies in the SCS can cause the thermocline to shallow
and thin, while anticyclonic eddies have the opposite effect (Chen et al.,
2011). Eddy activity in the SCS is related to local wind stress curl,
intrusion of the Kuroshio Current, and coastal baroclinic jets (Wang et al.,
2003; Hu et al., 2011). Cold-water cyclonic eddies can elevate the nutricline
into subsurface waters and drive enhanced phytoplankton production at levels
exceeding those in the winter. For example, the average integrated primary
production inside eddies in spring and in winter is 1090 and
550 mg C m<inline-formula><mml:math 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 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>, respectively (Chen, 2005; Chen et al., 2007b).
Modeling studies have reported that cyclonic eddies are significant nutrient
sources fueling the biological carbon pump in the SCS (Xiu and Chai, 2011).
Pigments determined by high-performance liquid chromatography have also shown
that phytoplankton assemblages relate to mesoscale eddies in the SCS (Huang
et al., 2010; Wang et al., 2016); however, how coccolithophore communities
respond to these regular oceanographic phenomena is still unclear.</p>
      <p>Decreasing ocean pH (termed ocean acidification), in response to increasing
atmospheric and seawater CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> levels, is a major concern for marine
calcifiers such as coccolithophores, as lower pH levels (and calcium
carbonate saturation levels, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> may lead to calcite
dissolution and/or make the process of calcite formation (calcification) more
difficult (Riebesell et al., 2000; Beaufort et al., 2011). Conflicting
results concerning coccolithophore calcification have been reported from both
experimental and field studies (e.g., Riebesell et al., 2000;
Iglesias-Rodriguez et al., 2008; Riebesell and Tortell, 2011; Meyer and
Riebesell, 2015). A recent study by Bach et al. (2015) found that laboratory
findings could be reconciled when an optimum-type response to bicarbonate ion
availability and pH was considered. In the field, different communities may
respond to different combinations of elevated pH and/or nutrient
availability, emphasizing the importance of species composition to community
responses and to the multivariate nature of the growth environment (Poulton
et al., 2011, 2014). Species-specific responses to ocean acidification are
evident from laboratory work (Langer et al., 2006, 2009) and in the
geological record (Gibbs et al., 2013; O'Dea et al., 2014), with regional
oceanographic settings also having an important influence (Beaufort et al.,
2011; Meier et al., 2014). Hence, it is necessary to understand how coccolith
(e.g., <italic>E. huxleyi</italic> strains in the SCS) size and morphology respond to
environmental factors in the oligotrophic and marginal SCS.</p>
      <p>In the present study, we performed an in situ investigation of
coccolithophores (species composition, coccolith biometry) in the upper
water column of the SCS in relation to the prevailing environmental
conditions. The aims of this research were (1) to examine coccolithophore
biogeography more clearly alongside their calcite concentration in the upper
water column and (2) to determine how coccolith morphology (i.e., <italic>E. huxleyi</italic>) responds to environmental variability (light, nutrients, and
carbonate chemistry) in a low-latitude marginal sea.</p>
</sec>
<sec id="Ch1.S2">
  <title>Materials and methods</title>
<sec id="Ch1.S2.SS1">
  <title>Field sampling</title>
      <p>A total of 72 water samples from 15 stations were collected during the R/V
<italic>Dongfanghong II</italic> cruise of the National Science Foundation (2014). At
most stations, five depths were sampled: 25, 50, 75, 100, and
150 m (Table 1). Water samples were not collected in the upper 5 m as this
was extremely nutrient depleted, with especially low chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>
concentrations (<uri>http://oceancolor.gsfc.nasa.gov/cms/</uri>) in summer
(Fig. 1). For each water sample, 3 L was collected via a
conductivity–temperature–depth (CTD) rosette sampler and filtered through
0.45 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m pore size 47 mm diameter nitrocellulose membrane filters
(Sartorius<sup>®</sup>) under gentle pressure. The
filters were rinsed to remove residual saline seawater, dried on an electric
heat platform (65 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, 10–15 min) and then stored in Petri dishes
wrapped with aluminum foil and stored frozen (<inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>20 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1" specific-use="star"><caption><p><bold>(a)</bold> Sampling stations in the South China Sea, superimposed
on the Aqua-MODIS (4 km) monthly average (May to August 2014) surface
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (mg m<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <bold>(b)</bold> Map of sea level anomaly (SLA)
and geostrophic flow on 28 June 2014. The positive SLA with clockwise flow
indicates anticyclonic eddies (AEs), and the negative SLA with anticlockwise
flow indicates cyclonic eddies (CEs).</p></caption>
          <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f01.pdf"/>

        </fig>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>Sampling dates, location, depth, and mixed layer depth (MLD) at each
station.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="6">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Station</oasis:entry>  
         <oasis:entry colname="col2">Date (yyyy/m/dd)</oasis:entry>  
         <oasis:entry colname="col3">Longitude</oasis:entry>  
         <oasis:entry colname="col4">Latitude</oasis:entry>  
         <oasis:entry colname="col5">Sampling depth</oasis:entry>  
         <oasis:entry colname="col6">MLD</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">(GMT <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>8)</oasis:entry>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4"/>  
         <oasis:entry colname="col5">(m)</oasis:entry>  
         <oasis:entry colname="col6">(m)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">D9</oasis:entry>  
         <oasis:entry colname="col2">2014/6/25 7:11</oasis:entry>  
         <oasis:entry colname="col3">119</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">F1</oasis:entry>  
         <oasis:entry colname="col2">2014/6/26 3:38</oasis:entry>  
         <oasis:entry colname="col3">118</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">24</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">G2</oasis:entry>  
         <oasis:entry colname="col2">2014/6/26 14:36</oasis:entry>  
         <oasis:entry colname="col3">117</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 45, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">12</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">H3</oasis:entry>  
         <oasis:entry colname="col2">2014/6/27 15:08</oasis:entry>  
         <oasis:entry colname="col3">116</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 60, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">11</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I1</oasis:entry>  
         <oasis:entry colname="col2">2014/6/20 0:52</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">19.5</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 100</oasis:entry>  
         <oasis:entry colname="col6">16</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I2</oasis:entry>  
         <oasis:entry colname="col2">2014/6/20 20:50</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">19</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">16</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I3</oasis:entry>  
         <oasis:entry colname="col2">2014/6/29 9:23</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">23</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">J1</oasis:entry>  
         <oasis:entry colname="col2">2014/6/29 20:35</oasis:entry>  
         <oasis:entry colname="col3">114</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">26</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">X3</oasis:entry>  
         <oasis:entry colname="col2">2014/6/30 6:58</oasis:entry>  
         <oasis:entry colname="col3">113</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">30</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">X4</oasis:entry>  
         <oasis:entry colname="col2">2014/6/30 18:01</oasis:entry>  
         <oasis:entry colname="col3">112</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">35</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">X5</oasis:entry>  
         <oasis:entry colname="col2">2014/7/1 5:10</oasis:entry>  
         <oasis:entry colname="col3">111</oasis:entry>  
         <oasis:entry colname="col4">18</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">17</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I4</oasis:entry>  
         <oasis:entry colname="col2">2014/7/9 8:23</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">17</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">18</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I5</oasis:entry>  
         <oasis:entry colname="col2">2014/7/9 1:54</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">16</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">(&lt; 25)</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I6</oasis:entry>  
         <oasis:entry colname="col2">2014/7/8 17:53</oasis:entry>  
         <oasis:entry colname="col3">115</oasis:entry>  
         <oasis:entry colname="col4">15</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100</oasis:entry>  
         <oasis:entry colname="col6">(&gt; 25)</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">I7</oasis:entry>  
         <oasis:entry colname="col2">2014/7/7 22:33</oasis:entry>  
         <oasis:entry colname="col3">114.67</oasis:entry>  
         <oasis:entry colname="col4">14</oasis:entry>  
         <oasis:entry colname="col5">25, 50, 75, 100, 150</oasis:entry>  
         <oasis:entry colname="col6">20</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS2">
  <title>Coccolithophore and coccolith counts</title>
      <p>A small piece (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0.5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 0.5 cm) of each filter was cut out and
mounted on glass slides using Norland Optical Adhesive (No. 74).
Coccolithophore cell counts and species identification was undertaken using
cross-polarized light microscopy (Olympus BX51). In samples with abundant
coccolithophore cells, individual cells (coccospheres) were counted from at
least 100 fields of view (FOVs, diameter of each FOV is 220 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m) up
to a total of 150 to 400 coccospheres. For samples with low abundance, around
50 extra FOVs were examined, which suggests a detection limit of
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0.27 cells mL<inline-formula><mml:math 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 a 95 % probability level (Bollmann et
al., 2002). For counts and morphological measurements of detached coccoliths,
a second piece of each filter was cut out (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0.5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 0.5 cm)
and mounted on an aluminum stub with double-sided conductive carbon tape and
coated with gold (see Poulton et al., 2011). A Leo 1450VP Scanning Electron
Microscopy (Carl Zeiss) with SmartSEM (V5.1) software was then used to
automatically capture images of consecutive FOVs from a 12 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 12 FOV
(each FOV was 4.054 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> mm<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> grid at a magnification
of <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula>5000, providing 144 images for analyses of detached coccolith
counting and biometry. Coccolithophore species identification by light
microscopy and scanning electron microscopy (SEM) followed Frada et
al. (2010), Young et al. (2003), and the Nannotax3 website
(<uri>http://ina.tmsoc.org/Nannotax3/</uri>). Coccosphere and coccolith abundance
was calculated using the following Eq. (1):

                <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mtext>coccosphere or coccolith  abundance</mml:mtext></mml:mrow></mml:mtd></mml:mtr><mml:mlabeledtr id="Ch1.E1"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mo>(</mml:mo><mml:msup><mml:mtext>cells coccoliths</mml:mtext><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">mL</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mi>N</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>×</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi>S</mml:mi><mml:mo>/</mml:mo><mml:mo>(</mml:mo><mml:mi>A</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>×</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi>V</mml:mi><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            where <inline-formula><mml:math display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula> is the number of coccospheres or coccoliths counted, <inline-formula><mml:math display="inline"><mml:mi>S</mml:mi></mml:math></inline-formula> is the
filtered area (45 mm diameter) on each filter, <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> is the area inspected
(<inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> number of FOV <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> area of 1 FOV), and <inline-formula><mml:math display="inline"><mml:mi>V</mml:mi></mml:math></inline-formula> is the filtered
water volume (mL).</p><?xmltex \hack{\newpage}?>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Coccosphere and coccolith biometry and calcite estimates</title>
      <p>Two distinguishable morphotypes of <italic>E. huxleyi</italic> (type A and type C)
were observed in the SEM images, with type A being the majority morphotype of
total <italic>E. huxleyi</italic> cell counting. The type C coccospheres were only found sporadically in some samples. Hence, the measurements of <italic>E. huxleyi</italic> biometry including distal shield length (DSL) and coccospheres
diameter (CD) were based only on morphotype A in this study. A total of 2560
<italic>E. huxleyi</italic> detached coccoliths (for DSL) and 102 intact coccospheres
(for DSL and CD) were measured across the study sites.</p>
      <p>In addition to <italic>E. huxleyi</italic>, coccolith lengths of all species were
measured to estimate bulk coccolith calcite concentration in the water column.
Individual coccolith calcite content (calcite mass) was calculated using
Eq. (2) adapted from Young and Ziveri (2000):
            <disp-formula id="Ch1.E2" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>m</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="normal">pg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">C</mml:mi><mml:mo>,</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mi mathvariant="normal">CaCO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mn>2.7</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>×</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>×</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mtext>DSL</mml:mtext><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where 2.7 is the density of calcite (pg C <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is
a shape constant determined for different species (Young and Ziveri, 2000), and DSL is the distal shield length of each coccolith (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m). For
whole coccospheres, the calcite content was estimated by multiplying the
calcite mass of a single coccolith (lying flat on the upper side of the
coccosphere) with an estimate of the number of coccoliths in the coccosphere
(e.g., 16 to 48 coccoliths in an <italic>E. huxleyi</italic> coccosphere in this
study). Numbers of coccoliths per coccosphere in the present study were also
estimated with reference to Boeckel and Baumann (2008). All the biometry
work was carried out on the basis of SEM images using ImageJ software
(<uri>http://rsb.info.nih.gov/ij/</uri>), following Poulton et al. (2011).</p>
      <p>Three coccolithophore species (<italic>Gladiolithus flabellatus</italic>,
<italic>Calciosolenia murrayi</italic>, and <italic>Algirosphaera robusta</italic>) present in
the SCS do not have <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values in Young and Ziveri (2000) or in
similar coccolith calcite estimates (e.g., Knappertsbusch and Brummer, 1995;
Beaufort and Heussner, 1999). For the body coccolith of <italic>G. flabellatus</italic>, a <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value is estimated as 0.0016, adjusted from
<italic>Florisphaera profunda</italic> (0.04) and based on their similar rectangle
shapes. For <italic>C. murrayi</italic>, the rhomboid-shaped coccosphere is
dimorphic, having both body coccoliths and narrow coccoliths around the
apical opening (Young et al., 2003). Body coccolith lengths in <italic>C. murrayi</italic> range from 2.2 to 2.6 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m, with the mean length / width ratio
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 3.045 in our samples, and the thickness is about 0.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m (from Malinverno, 2004). From these morphological parameters, the
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value we estimated is 0.027. For <italic>A. robusta</italic>, each
coccolith contains two parts: a base and a protrusion. The former is similar
to a small <italic>Syracosphaera</italic> coccolith, with a <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of
0.015 (Young and Ziveri, 2000) and for the latter <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value we
calculated a cylindroid-like volume which we estimated as 0.045. Combining
these two estimates gave a <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of 0.06 for <italic>A. robusta</italic> in this study.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><caption><p>Temperature (<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) profiles in zonal <bold>(a)</bold> and
meridional <bold>(b)</bold> sections. Variation of isotherm indicates
anticyclonic eddies (AEs) and cyclonic eddies (CEs), respectively. Profiles are
drawn with Ocean Data View software (Schlitzer, 2015).</p></caption>
          <?xmltex \igopts{width=426.791339pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f02.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><caption><p>Vertical profiles of <bold>(a)</bold> percentage of surface
photosynthetically active radiation (PAR), <bold>(b)</bold> fluorescence
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (mg m<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, <bold>(c)</bold> nitrate <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrite, and
<bold>(d)</bold> phosphate concentration (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. Euphotic zone
depth (Zeu) is defined as 1 % of surface irradiance penetration. The
black lines denote moving average of 30 grid points of cyclonic eddy (CE,
<bold>a</bold>) and anticyclonic eddy (AE, <bold>b</bold>) stations.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f03.pdf"/>

        </fig>

</sec>
<sec id="Ch1.S2.SS4">
  <title>Environmental parameters</title>
      <p>Seawater temperature, salinity, and chlorophyll fluorescence were taken from
the CTD. For stations I4, I5, I6, and I7, CTD problems led to discontinuous
temperature and salinity data. Mixed layer depths (MLDs) were taken as the
depth where the temperature difference was &gt; 0.5 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C with
respect to surface waters (&lt; 5 m; Painter et al., 2010), while for
stations I4 to I6, the MLDs were only roughly determined according to vertical
temperature profiles (see Fig. 2b). Euphotic zone depth is defined as the
depth to which 1 % of surface irradiance penetrates. Photosynthetically
active radiation (PAR) through the water column is calculated following
Eq. (3):
            <disp-formula id="Ch1.E3" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mtext>PAR</mml:mtext><mml:mi>Z</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mtext>PAR</mml:mtext><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>×</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi>exp⁡</mml:mi><mml:mo>(</mml:mo><mml:mo>-</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>×</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi>Z</mml:mi><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, the vertical diffuse attenuation coefficient, is
estimated by the following Eq. (4) from Wei (2005):
            <disp-formula id="Ch1.E4" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>0.027</mml:mn><mml:mo>+</mml:mo><mml:mn>0.252</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>×</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mi>c</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the beam attenuation recorded by the CTD.
Identification of eddy activity was according to the temperature sections
(Fig. 2) and altimeter data on sea level anomalies (SLAs) and geostrophic flow
from the AVISO website (<uri>http://www.aviso.altimetry.fr/en/home.html</uri>).</p>
      <p>Macronutrient (nitrate <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrite, phosphate) concentrations were
determined immediately on board with colorimetric methods, using a Technicon
AA3 Auto-Analyzer (Bran-Lube). The detection limits for nitrate <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrite
and phosphate are 0.1 and 0.08 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math 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>, respectively.
Seawater carbonate parameters (total alkalinity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and
dissolved inorganic carbon (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> were determined following the
updated Joint Global Ocean Flux Study protocols (Dickson et al., 2007). Water
samples for measurements were poisoned with saturated mercuric chloride
solution and stored in the dark before analysis. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was measured on
board within 2 days of sampling and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was measured within 2 months. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was measured by collecting and quantifying the
CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> released from the sample upon acidification with a nondispersive
infrared detector (LI-COR<sup>®</sup> 7000).
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was measured by potentiometric Gran titration. The accuracies
of the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> measurements were calibrated against
the certified reference materials provided by A. G. Dickson of the Scripps
Institution of Oceanography. Carbonate ion concentration, carbonate calcium
saturation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, and pH were calculated by CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>SYS excel
macro (Pierrot et al., 2006) from nutrients, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>,
temperature, and salinity.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <title>Statistical analysis</title>
      <p>Multivariate data analysis was performed to further examine the
coccolithophore composition across the study sites using the PRIMER-E (v. 6.0)
program (Clarke and Warwick, 2001). Before analysis, the sites of zero
coccolithophore abundance and those at 150 m were removed and the absolute
coccolithophore abundance data were then treated by square-root transformation.
With these abundance data, a Bray–Curtis similarity matrix was constructed and
analyzed via hierarchical cluster analysis (HCA) together with nonmetric
multidimensional scaling (nMDS).</p>
      <p>Principal component analysis was also performed based on the z-score
normalized environmental parameters to evaluate the main controlling
factors. Pearson's product-moment correlations and Spearman's rank
correlation were used to examine potential relationships between
coccolithophore data and environmental factors. One-way ANOVA was performed
to assess the coccolith length differences between samples. These
statistical analyses were carried out using the PAST software (Hammer et al.,
2001).</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
<sec id="Ch1.S3.SS1">
  <title>Physicochemical settings</title>
      <p>A conspicuous deep chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> maximum (DCM) was present throughout,
ranging from <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 50 to 75 m in depth (Fig. 3). Total nitrogen and
phosphate concentrations were below the limit of quantitation in the upper
25 m. A nitrogen concentration of 1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math 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> was defined as
the threshold of the nitricline and also the nutricline (Mullin, 1998), which was within the range of &lt; 50 to 75 m (Fig. 3). All stations were stratified,
with shallow mixed layers, ranging from 11 to 35 m. According to the
vertical temperature profiles, SLA map, and geostrophic flows (Figs. 1b and
2), two anticyclonic eddies (labeled herein as AEs) and one cyclonic eddy
(CE) were present across the 18<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N section, with stations X4, X3, and
J1 located in AE1, F1, and D9 located in AE2, and I3 and H3 located in CE. The
nutricline and DCM changed with the variability of oceanographic settings;
e.g., they shallowed in the CE stations and deepened in the AE stations
(Fig. 3). Euphotic zone depths ranged from 90 to 100 m, except at stations
I1 and I2, where the euphotic zone depth was <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 70 m. The
detailed SLA and geostrophic flow maps during sampling dates can be found in
the Supplement.</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Coccolithophore community</title>
      <p>The average coccolithophore cell abundance was 11.82 cells mL<inline-formula><mml:math 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>,
ranging from &lt; 0.27 to 83.67 cells mL<inline-formula><mml:math 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> across the sampling
sites. The highest cell abundance was found at station I3 at a depth of
50 m. At each station, the lowest cell abundances were found at 25 and/or
150 m, whereas the depth with the highest abundances was at 50 and/or
75 m, in close proximity to the DCM. A total of 17 coccolithophore taxa were
counted (Table 2) across the study sites.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Nonmetric multidimensional scaling (nMDS) ordination of stations
at different depths, based on Bray–Curtis similarity. The 0.13 stress of
two-dimensional ordination can provide a good interpretation for community
groups (Clarke and Warwick, 2001). The blue dashed lines indicate different
divisions at 40 % (dis)similarity; the divisions are determined by cluster
analysis, using the same resemblance as nMDS. CE: cyclonic eddy; AE:
anticyclonic eddy.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f04.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p>Coccolithophore abundance (cells mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> of three groups at sampling stations. “LPZ” specifically indicates three species: <italic>F. profunda</italic>, <italic>A. robusta</italic>, and <italic>G. flabellatus</italic>. “UPZ”
specifically indicates <italic>Umbellosphaera</italic> spp., <italic>D. tubifera</italic>, and <italic>R. clavigera</italic>.</p></caption>
          <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f05.pdf"/>

        </fig>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p>Coccolithophore species composition in Group 1, Group 2, and Group 3.
<inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula>: mean relative abundance; <inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula>: occurrence frequency. Bold numbers
indicate the representative species in their groups.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="7">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right" colsep="1"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right" colsep="1"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:colspec colnum="7" colname="col7" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry rowsep="1" namest="col2" nameend="col3" align="center" colsep="1">Group 1 </oasis:entry>  
         <oasis:entry rowsep="1" namest="col4" nameend="col5" align="center" colsep="1">Group 2 </oasis:entry>  
         <oasis:entry rowsep="1" namest="col6" nameend="col7" align="center">Group 3 </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col6"><inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col7"><inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Algirosphaera robusta</italic></oasis:entry>  
         <oasis:entry colname="col2">0.39</oasis:entry>  
         <oasis:entry colname="col3">23.53</oasis:entry>  
         <oasis:entry colname="col4">2.22</oasis:entry>  
         <oasis:entry colname="col5">66.67</oasis:entry>  
         <oasis:entry colname="col6"><bold>19.78</bold></oasis:entry>  
         <oasis:entry colname="col7"><bold>92.86</bold></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Florisphaera profunda</italic></oasis:entry>  
         <oasis:entry colname="col2">0.35</oasis:entry>  
         <oasis:entry colname="col3">17.65</oasis:entry>  
         <oasis:entry colname="col4">1.34</oasis:entry>  
         <oasis:entry colname="col5">41.67</oasis:entry>  
         <oasis:entry colname="col6"><bold>43.81</bold></oasis:entry>  
         <oasis:entry colname="col7"><bold>100.00</bold></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Gladiolithus flabellatus</italic></oasis:entry>  
         <oasis:entry colname="col2">0.00</oasis:entry>  
         <oasis:entry colname="col3">0.00</oasis:entry>  
         <oasis:entry colname="col4">0.00</oasis:entry>  
         <oasis:entry colname="col5">0.00</oasis:entry>  
         <oasis:entry colname="col6"><bold>1.66</bold></oasis:entry>  
         <oasis:entry colname="col7"><bold>60.71</bold></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Emiliania huxleyi</italic></oasis:entry>  
         <oasis:entry colname="col2"><bold>36.97</bold></oasis:entry>  
         <oasis:entry colname="col3"><bold>94.12</bold></oasis:entry>  
         <oasis:entry colname="col4"><bold>66.84</bold></oasis:entry>  
         <oasis:entry colname="col5"><bold>100.00</bold></oasis:entry>  
         <oasis:entry colname="col6"><bold>22.65</bold></oasis:entry>  
         <oasis:entry colname="col7"><bold>92.86</bold></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Gephyrocapsa oceanica</italic></oasis:entry>  
         <oasis:entry colname="col2">2.29</oasis:entry>  
         <oasis:entry colname="col3">41.18</oasis:entry>  
         <oasis:entry colname="col4"><bold>10.23</bold></oasis:entry>  
         <oasis:entry colname="col5"><bold>91.67</bold></oasis:entry>  
         <oasis:entry colname="col6">1.65</oasis:entry>  
         <oasis:entry colname="col7">46.43</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Gephyrocapsa ericsonii</italic></oasis:entry>  
         <oasis:entry colname="col2">6.20</oasis:entry>  
         <oasis:entry colname="col3">52.94</oasis:entry>  
         <oasis:entry colname="col4">6.20</oasis:entry>  
         <oasis:entry colname="col5">50.00</oasis:entry>  
         <oasis:entry colname="col6">2.61</oasis:entry>  
         <oasis:entry colname="col7">32.14</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Umbellosphaera irregularis</italic></oasis:entry>  
         <oasis:entry colname="col2"><bold>34.35</bold></oasis:entry>  
         <oasis:entry colname="col3"><bold>94.12</bold></oasis:entry>  
         <oasis:entry colname="col4">0.86</oasis:entry>  
         <oasis:entry colname="col5">41.67</oasis:entry>  
         <oasis:entry colname="col6">0.24</oasis:entry>  
         <oasis:entry colname="col7">7.14</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Umbellosphaera tenuis</italic></oasis:entry>  
         <oasis:entry colname="col2">2.14</oasis:entry>  
         <oasis:entry colname="col3">47.06</oasis:entry>  
         <oasis:entry colname="col4">0.10</oasis:entry>  
         <oasis:entry colname="col5">16.67</oasis:entry>  
         <oasis:entry colname="col6">0.00</oasis:entry>  
         <oasis:entry colname="col7">0.00</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Discosphaera tubifera</italic></oasis:entry>  
         <oasis:entry colname="col2"><bold>4.41</bold></oasis:entry>  
         <oasis:entry colname="col3"><bold>82.35</bold></oasis:entry>  
         <oasis:entry colname="col4">0.11</oasis:entry>  
         <oasis:entry colname="col5">8.33</oasis:entry>  
         <oasis:entry colname="col6">0.00</oasis:entry>  
         <oasis:entry colname="col7">0.00</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Rhabdosphaera clavigera</italic></oasis:entry>  
         <oasis:entry colname="col2">0.82</oasis:entry>  
         <oasis:entry colname="col3">23.53</oasis:entry>  
         <oasis:entry colname="col4">0.04</oasis:entry>  
         <oasis:entry colname="col5">8.33</oasis:entry>  
         <oasis:entry colname="col6">0.00</oasis:entry>  
         <oasis:entry colname="col7">0.00</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Calcidiscus leptoporus</italic></oasis:entry>  
         <oasis:entry colname="col2">0.82</oasis:entry>  
         <oasis:entry colname="col3">17.65</oasis:entry>  
         <oasis:entry colname="col4">1.53</oasis:entry>  
         <oasis:entry colname="col5">58.33</oasis:entry>  
         <oasis:entry colname="col6">0.96</oasis:entry>  
         <oasis:entry colname="col7">35.71</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Oolithotus fragilis</italic></oasis:entry>  
         <oasis:entry colname="col2">3.64</oasis:entry>  
         <oasis:entry colname="col3">35.29</oasis:entry>  
         <oasis:entry colname="col4">6.95</oasis:entry>  
         <oasis:entry colname="col5">83.33</oasis:entry>  
         <oasis:entry colname="col6">3.87</oasis:entry>  
         <oasis:entry colname="col7">78.57</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Helicosphaera carteri</italic></oasis:entry>  
         <oasis:entry colname="col2">1.05</oasis:entry>  
         <oasis:entry colname="col3">58.82</oasis:entry>  
         <oasis:entry colname="col4">0.21</oasis:entry>  
         <oasis:entry colname="col5">25.00</oasis:entry>  
         <oasis:entry colname="col6">0.03</oasis:entry>  
         <oasis:entry colname="col7">3.57</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Syracosphaera</italic> spp.</oasis:entry>  
         <oasis:entry colname="col2">3.92</oasis:entry>  
         <oasis:entry colname="col3">94.12</oasis:entry>  
         <oasis:entry colname="col4">1.56</oasis:entry>  
         <oasis:entry colname="col5">83.33</oasis:entry>  
         <oasis:entry colname="col6">1.55</oasis:entry>  
         <oasis:entry colname="col7">53.57</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Umbilicosphaera sibogae</italic></oasis:entry>  
         <oasis:entry colname="col2">0.45</oasis:entry>  
         <oasis:entry colname="col3">17.65</oasis:entry>  
         <oasis:entry colname="col4">0.71</oasis:entry>  
         <oasis:entry colname="col5">33.33</oasis:entry>  
         <oasis:entry colname="col6">0.22</oasis:entry>  
         <oasis:entry colname="col7">14.29</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Calciosolenia</italic> spp.</oasis:entry>  
         <oasis:entry colname="col2">0.49</oasis:entry>  
         <oasis:entry colname="col3">23.53</oasis:entry>  
         <oasis:entry colname="col4">0.48</oasis:entry>  
         <oasis:entry colname="col5">58.33</oasis:entry>  
         <oasis:entry colname="col6">0.41</oasis:entry>  
         <oasis:entry colname="col7">21.43</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"><italic>Michaelsarsia</italic> spp.</oasis:entry>  
         <oasis:entry colname="col2">1.71</oasis:entry>  
         <oasis:entry colname="col3">35.29</oasis:entry>  
         <oasis:entry colname="col4">0.61</oasis:entry>  
         <oasis:entry colname="col5">41.67</oasis:entry>  
         <oasis:entry colname="col6">0.54</oasis:entry>  
         <oasis:entry colname="col7">25.00</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>The nMDS ordination (Fig. 4) shows that at a level of 40 %
(dis)similarity in the HCA (see Supplement), three groups of water samples
occurred: Group 1 mainly contained <italic>E. huxleyi</italic> and
<italic>Umbellosphaera irregularis</italic>, with the lowest average cell
concentrations of all the groups identified (8.57 cells mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, and
represented the shallowest samples (25 and 50 m). Most of the samples were
located at 25 m and some at 50 m, (Fig. 5) and were representative of
oligotrophic conditions in the upper mixed layer. Group 2 was dominated by
<italic>E. huxleyi</italic>, with the highest average cell concentration
(27.38 cells mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> of all the groups. Samples in this group were
usually located at depths between 45 and 75 m (Fig. 5), around 25 m below
the MLD and representing the DCM, with elevated nutrients. Group 3 included
taxa representing the lower photic zone (<italic>A. robusta</italic>, <italic>F. profunda</italic>), with <italic>E. huxleyi</italic> also abundant in most samples. Samples
in Group 3 were found at 75 and 100 m depth (Fig. 5), in which mean cell
concentrations were 17.43 and 9.04 cells mL<inline-formula><mml:math 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>, respectively.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <title>Estimates of coccolith and coccosphere calcite</title>
      <p>The mean concentration of detached coccoliths was 158 coccoliths mL<inline-formula><mml:math 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>,
with a range of 0 to 673 coccoliths mL<inline-formula><mml:math 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 detached
coccolith concentration was observed at station F1 at 75 m, corresponding to
the highest cell number (22.87 cells mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> at this station. However,
this pattern was not common at some stations. For example, the second-highest
detached coccolith concentration (623 coccoliths mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> was found at
station D9 at 150 m, the easternmost station sampled (Fig. 1), where
coccosphere concentration was low (1.87 cells mL<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. It is unlikely
that such high abundances of detached coccoliths in deep layers of the water
column could be produced in situ when cell abundances are so low, and hence
these features may indicate either lateral or vertical transport.</p>
      <p>Based on coccosphere and detached coccolith concentrations, estimated total
calcite concentrations ranged from <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0 to 5258.1 pg C mL<inline-formula><mml:math 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>, with
a cruise average of 1508.3 pg C mL<inline-formula><mml:math 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>. Estimated total calcite
concentrations roughly mirrored detached coccolith concentrations (Fig. 6;
Spearman's rank correlation, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>0.81</mml:mn></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01,
<inline-formula><mml:math display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 67), highlighting the contribution of detached coccoliths to
particulate calcite in the water column. Our estimated calcite concentrations
were in the same range as those estimated by Beaufort et al. (2008) in the
southeast Pacific (2224 pg C mL<inline-formula><mml:math 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). The cruise average
calcite concentrations based on three important coccolithophore species
(<italic>E. huxleyi</italic>, <italic>Gephyrocapsa oceanica</italic>, and <italic>F. profunda</italic>) which dominate surface sediments (Cheng and Wang, 1997; Fernando et
al., 2007) and deep-sea coccolith fluxes (Jin et al., unpublished) in the SCS were
273.0, 112.1, and 391.3 pg C mL<inline-formula><mml:math 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>, respectively. Their average relative
contributions to water-column calcite were also estimated: <italic>E. huxleyi</italic> (17.04 %), <italic>G. oceanica</italic> (7.00 %), and <italic>F. profunda</italic> (24.42 %) contributed to around half of water-column calcite
concentrations (Fig. 7). The depth distribution of these species
contributions to total calcite matched well with their average depth
distribution across the study area: <italic>E. huxleyi</italic> and <italic>G. oceanica</italic> contributions were highest in the upper water column (25 and
50 m), and <italic>F. profunda</italic> contributions were highest at depths of 75
and 100 m.</p>
</sec>
<sec id="Ch1.S3.SS4">
  <?xmltex \opttitle{\textit{Emiliania huxleyi} biometry}?><title><italic>Emiliania huxleyi</italic> biometry</title>
      <p>From all the samples analyzed, the average DSL of
<italic>E. huxleyi</italic> type A was 2.96 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m, with an overall standard
deviation of 0.39 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m. Pearson's product-moment correlations showed
the relationships between average DSL, nutrients (nitrite <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrate,
phosphate), carbonate chemistry (pH, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, and temperature (<inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>) (<inline-formula><mml:math display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 29, Table 3). Statistically significant (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01) correlations were found between DSL, total nitrogen
(nitrite <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrate), and phosphate (positive) and between pH and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (negative), whereas no correlation occurred between DSL,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>. The mean coccosphere diameter of <italic>E. huxleyi</italic>
across all those measured was 6.41 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m, with a standard deviation of
0.95 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m. The average number of coccoliths estimated per coccosphere
was 32, with an overall range of 16 to 48. CD showed
a statistically significant positive relationship with DSL (Pearson's
<inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.71, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01, <inline-formula><mml:math display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 102) and coccolith number per
sphere (<inline-formula><mml:math display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula>) (Pearson's <inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.87, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01, <inline-formula><mml:math display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 102),
and the correlation was also significant between DSL and N (Pearson's
<inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.51, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01, <inline-formula><mml:math display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 102). A linear regression gave
a coccosphere diameter of CD <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.205  <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> DSL <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> 1.664 (<inline-formula><mml:math 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:mrow></mml:math></inline-formula> 0.49, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01), and a binary regression equation also gave a coccosphere diameter of CD <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 1.205
 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> DSL <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> 0.106 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> 0.096 (<inline-formula><mml:math 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:mrow></mml:math></inline-formula> 0.85, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p>Coccolithophore-based calcite concentration <bold>(a)</bold> and
detached coccolith concentration <bold>(b)</bold> in zonal and meridional
sections.</p></caption>
          <?xmltex \igopts{width=483.69685pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f06.pdf"/>

        </fig>

</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <title>Coccolithophore biogeography in the South China Sea</title>
      <p>In the context of the coccolithophore biogeographical zones of Winter et al.
(1994), the coccolithophore assemblages investigated in the SCS belong to
the <italic>tropical</italic> zone, comprising <italic>E. huxleyi</italic>, <italic>G. oceanica</italic>, <italic>Gephyrocapsa ericsonii</italic>, <italic>Oolithotus fragilis</italic>,
<italic>U. irregularis</italic>, <italic>F. profunda</italic>, and <italic>A. robusta</italic>.
<italic>Reticulofenestra sessilis</italic> was also sporadically found at 75 m depth
at sampling stations, and this species is reported to be exclusively found in
lower photic water of the tropical zone, where it may form symbioses
with diatoms (i.e., <italic>Thalassiosira</italic> species) (Winter et al., 1994;
Young et al., 2003; Jordan, 2012). The coccolithophore flora of the SCS is
similar to the “high temperature” and “warm oligotrophic” assemblages
in the equatorial Pacific Ocean (Hagino et al., 2000).</p>
      <p>The two dominant species in our samples from the SCS were <italic>E. huxleyi</italic>
and <italic>F. profunda</italic>, species representative of the upper and lower
photic zone floral groups (Winter et al. 1994). These floral groups both live
within the euphotic zone (&gt; 1 % surface irradiance), which is
about 100 m in summer in the SCS. However, in the western Pacific warm pool
(stratified waters) and subtropical gyres of the Pacific and Atlantic oceans,
species <italic>F. profunda</italic> are found much deeper (150 to 250 m) in the
water column (Hagino et al., 2000; Boeckel and Baumann, 2008; Beaufort et
al., 2008). These differences are undoubtedly linked to differences between
the SCS and open ocean in terms of the depths of the thermocline and nutricline,
implying that the SCS is relatively eutrophic when compared with tropical and
subtropical settings at a similar latitude.</p>
<sec id="Ch1.S4.SS1.SSS1">
  <title>Upper photic zone (UPZ) assemblage</title>
      <p>In our nMDS analysis, the UPZ
assemblage (Winter et al., 1994) was represented by Groups 1 and 2, found at
25 and 50 m in the SCS. These two groups have different species composition
in our analysis; for example, Group 1 included umbelliform species, i.e.,
<italic>U. irregularis</italic>, which are considered <inline-formula><mml:math display="inline"><mml:mi>K</mml:mi></mml:math></inline-formula> selected (specialist)
species (Young, 1994), and this agrees with previous work (e.g., Okada and
Honjo, 1975). The UPZ assemblage is commonly observed in well-stratified,
oligotrophic, warm surface waters in the western Pacific warm pool (Hagino et
al., 2000). In the SCS, <italic>U. irregularis</italic> was mostly found at stations
with deep mixed layers, deep nutriclines, and extremely low nutrients in
surface waters. In comparison, Group 2 occurred at stations with shallower
mixed layers and nutriclines and hence potentially elevated nutrient
supplies, and coccolithophores in this group were most abundant and diverse,
which indicates that this community was slightly productive when compared
with those in other groups. The <italic>E. huxleyi</italic> dominance contradicts
other studies in the SCS in summer, such as Okada and Honjo (1975) and Sun et
al. (2011), who found that <italic>G. oceanica</italic> was the dominant species (30
to 100 % of total cell numbers) in the western and southern parts of the
SCS. Differences between this study and others could relate to the influence
of the Asian summer monsoon on the western and southern SCS, where the
southwesterly wind causes a wind-driven upwelling system off the east coast
of Vietnam (Liu et al., 2002; Xie et al., 2003; Ning et al., 2004).
<italic>G. oceanica</italic> is considered a more eutrophic and coastal species
(Andruleit and Rogalla, 2002; Andruleit et al., 2003), and hence it
contributed less to coccolithophore cells in the central and northern part of
SCS, where summer-monsoon-induced upwelling or water mixing is weak.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7" specific-use="star"><caption><p>The relative contribution of <italic>E. huxleyi</italic> <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> <italic>G. oceanica</italic> and <italic>F. profunda</italic> to coccolithophore-based calcite
concentration in the water column at all stations <bold>(a)</bold>; at I1, I2, I3, I4,
I5, and H3 <bold>(b)</bold>; and at X3, X4, I6, I7, F1, and D9 <bold>(c)</bold>. The solid lines
denote moving average of 30 grid points. <bold>(d)</bold> Yearly averaged
coccolith relative abundance and their contribution to coccolith-based
calcite in sediment trap (117.46<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> E 20<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 500 m) in the
South China Sea (Jin et al., unpublished).</p></caption>
            <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f07.pdf"/>

          </fig>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><caption><p>Pearson's product-moment correlations (<inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>) between mean distal
shield length (DSL) of <italic>E. huxleyi</italic>, principal component 1 (PC-1)
scores and environmental parameters: nitrate <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrite (N), phosphate
(P), pH, total alkalinity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, CaCO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> saturation
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, and temperature (<inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>) (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn>29</mml:mn></mml:mrow></mml:math></inline-formula>). The principal component
analysis is based on all the environmental parameters, with a PC-1
contribution of 76.59 % to total variance. <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi><mml:mn> 0.05</mml:mn></mml:mrow></mml:math></inline-formula>; <inline-formula><mml:math 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 display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi><mml:mn> 0.01</mml:mn></mml:mrow></mml:math></inline-formula>.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <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:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Mean DSL</oasis:entry>  
         <oasis:entry colname="col3">PC-1 (76.59 %)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">N</oasis:entry>  
         <oasis:entry colname="col2">0.601<inline-formula><mml:math 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="col3"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.967<inline-formula><mml:math 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:row>
       <oasis:row>  
         <oasis:entry colname="col1">P</oasis:entry>  
         <oasis:entry colname="col2">0.579<inline-formula><mml:math 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="col3"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.965<inline-formula><mml:math 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:row>
       <oasis:row>  
         <oasis:entry colname="col1">pH</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.526<inline-formula><mml:math 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="col3">0.804<inline-formula><mml:math 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:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">T</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2">0.274</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.671<inline-formula><mml:math 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:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.395<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.958<inline-formula><mml:math 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:row>
       <oasis:row>  
         <oasis:entry colname="col1"><inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.21</oasis:entry>  
         <oasis:entry colname="col3">0.842**</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>Morphotype A was the dominant morphotype of <italic>E. huxleyi</italic> in the SCS.
Different morphotypes of <italic>E. huxleyi</italic> can be distinguished by
coccolith characteristics such as DSL, element widths, and features of the
central area (e.g., Young et al., 2003; Hagino et al., 2011) and may be
considered different ecotypes with different temperature and nutrient
preferences (Cook et al., 2011; Poulton et al., 2011; Hagino et al., 2011;
Saavedra-Pellitero et al., 2014). In general, <italic>E. huxleyi</italic> type A
shows a warmer-water preference than type B and other type B derivatives (C,
B/C). In our observations, type C <italic>E. huxleyi</italic> coccospheres or coccoliths
were only found sporadically in SEM images, and the predominant occurrences
of morphotype A could be related to the prevailing high sea-surface
temperature (&gt; 26 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) in the study area. The southern
part of SCS is also within the western Pacific warm pool, where sea-surface temperature is consistently &gt; 28 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
all year round (Yan et al., 1992).</p>
</sec>
<sec id="Ch1.S4.SS1.SSS2">
  <title>Lower photic zone (LPZ) assemblage</title>
      <p>In the present study, the LPZ was
represented by Group 3, which included typical LPZ species (<italic>F. profunda</italic>, <italic>A. robusta</italic>, and <inline-formula><mml:math display="inline"><mml:mi>G</mml:mi></mml:math></inline-formula>. <italic>flabellatus</italic>) and was found
between 75 and 100 m. Group 3 occurred above, at, or near the depth where
1 % of surface irradiance penetrated (i.e., base of the euphotic zone).
In other tropical oceans, the LPZ assemblage dwells deeper than the base of
the euphotic zone (Hagino et al., 2000; Boeckel and Baumann, 2008; Beaufort
et al., 2008). In the northern Arabian Sea, <italic>F. profunda</italic> inhabits
shallower waters and is found across a wider depth range (10 to 80 m)
(Andruleit et al., 2003). It is worth noting that, as in the SCS, the Arabian
Sea is strongly controlled by a monsoonal system (Indian monsoon) and is
considered relatively eutrophic (Andruleit and Rogalla, 2002; Andruleit et
al., 2003). Hence, it can be inferred that neither water depth nor light
availability is a limiting factor for <italic>F. profunda</italic> (and/or other LPZ
species) in the SCS, but rather nutrient availability is important; the
nutricline is relatively shallow (50 to 75 m) even in the oligotrophic
summer in the SCS.</p>
</sec>
</sec>
<sec id="Ch1.S4.SS2">
  <title>The response of coccolithophores to eddies in the South China
Sea</title>
      <p>Mesoscale eddies have a strong influence on productivity and ecosystem
structure in the SCS (Chen et al., 2007b; Lin et al., 2010; Wang et al.,
2016). Previous measurements in the SCS have shown that integrated primary
production in cyclonic eddies can be 2–3-fold higher relative to the outside
of eddies (Chen et al., 2007b). Modeling results have also highlighted how
new production can be <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 30 % higher
or lower, relative to outside of eddies, in cyclonic or anticyclonic eddies, respectively (Xiu and Chai,
2011).</p>
      <p>Results from nMDS, HCA, and eddy settings in the 18<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N section
clearly show that the coccolithophore communities in the SCS were strongly
coupled with eddy occurrences (Fig. 5). In the cyclonic eddy (I3, H3),
Group 2 occurred in ranges of 25 to 50 m depth and Group 3 occurred within
layers from 75 to 100 m. Comparatively, at stations (X5, G2) with “normal”
(non-eddy) conditions, three groups sequentially occurred in the
water column: Group 1 at 25 m, Group 2 at 50 m, and Group 3 between 75 and 100 m depth. In anticyclonic eddies, there were two patterns: one with
Group 1 distributed within a wider depth range (from 25 to 50 m) and
Group 3 only within a 100 m layer; the other was that Group 2 was absent,
and the maximum coccolithophore abundance depth was deep and belonged to
Group 3, which was dominated by LPZ assemblages (e.g., <italic>F. profunda</italic>).
This variation highlights the importance of the ecological effects of eddies on
the coccolithophore community's depth distribution through the water column.
As the anticyclonic eddy (cyclonic eddy) centers lead to convergence
(divergence) of the adjacent waters, they deepen (shoaling) the nutricline and
creating more oligotrophic (slightly eutrophic) conditions in the water
column which favor distinct coccolithophore assemblages (Fig. 8).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8"><caption><p>Schematic showing the coccolithophore communities in an anticyclonic
eddy and a cyclonic eddy.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f08.pdf"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9" specific-use="star"><caption><p><italic>E. huxleyi</italic> distal shield length plot versus coccosphere
diameter <bold>(a)</bold> in the present study with comparison with those from
other field and culturing samples (Triantaphyllou et al., 2010; Henderiks et
al., 2012; Bach et al., 2012; Müller et al., 2012). These <italic>E. huxleyi</italic> biometry data are derived from Fig. 6 in Müller et al. (2012).
<bold>(b)</bold> Scatterplot of single coccolith weight (calculated from Eq. 2)
and number of coccoliths per coccosphere (<inline-formula><mml:math display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula>), showing the particulate
inorganic carbon (PIC) per cell.</p></caption>
          <?xmltex \igopts{width=426.791339pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f09.pdf"/>

        </fig>

      <p>Due the discontinuous sampling dates (Table 1) and low resolution of
environmental data at some stations, the meridional section may not be
suitable for assessing the eddy impacts on coccolithophore communities. For
example, at I6 and I7, stations were not characteristic of anticyclonic
eddies based on the SLA and geostrophic flow map; however, the
coccolithophore community vertical composition or structure is similar to those
in the anticyclonic eddies. This may be due to the deeper nutricline in the
central basin of the SCS, even if the water-column structure had not been
modulated by eddies in our investigation. Another example is stations I1 and
I2, for which the coccolithophore groups agreed with those in the cyclonic
eddies. Likewise, this was also not characteristic of the cyclonic eddies, as
shown by SLA and geostrophic flow (Supplement). At stations I1 and I2, the
euphotic zone depth was relatively shallow (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 70 m), with more light
attenuation from suspended particles, which could be caused by elevated
particle production. This finding corresponds to the station locations at
the edge of the anticyclonic eddy where particulate organic carbon (POC)
fluxes can be 2–4-fold higher than those in adjacent oligotrophic waters
(Zhou et al., 2013; Shih et al., 2015). For station I4, the case was similar
to I1 and I2, as it was located at the edge of two large anticyclonic eddies
(supplement). The horizontal advection, for water mass balance, can result in
the elevated nutricline in anticyclonic eddy edges and, hence, the
enhancement of POC production and export (Zhou et al., 2013).</p>
      <p><?xmltex \hack{\newpage}?>Station I5 had another distinctive arrangement of species assemblages, which
was the opposite of that found at the other stations sampled (Fig. 5); Group 2
was found at 25 m while Group 1 was at 50 m. Examination of the temperature
profile shows that the 29.5 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C isotherm was shallow and domed, while
the 22.5 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C isotherm was pushed deeper into the water column
(Fig. 2b). Filters collected at 25 and 50 m from I5 also had lots of diatom
fragments and relatively elevated coccolithophore abundances (21.75 and
22.59 cells mL<inline-formula><mml:math 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 25 and 50 m, respectively). We suggest that this
feature may represent a mode-water eddy, as described by McGillicuddy et
al. (2007) in the northeast subtropical Atlantic Ocean. McGillicuddy et
al. (2007) observed elevated phytoplankton production (i.e., a diatom bloom)
in a mode-water eddy, which led to local changes in the zooplankton community
composition (McGillicuddy et al., 2007; Eden et al., 2009).</p>
</sec>
<sec id="Ch1.S4.SS3">
  <title>Calcite concentrations in the South China Sea</title>
      <p>The discrete estimates of bulk coccolith calcite roughly covaried with
coccolith and coccolithophore concentration in the water column, with peak
concentrations around the DCM. Excluding the maximum calcite concentration in
the DCM, another peak was also found in deeper water at some stations, for
example at 150 m in F1 and D9 and 100 and 150 m in I7, where the cell
concentrations were low and calcite was nearly entirely contributed by detached
coccoliths. In addition, the relative calcite contribution of different taxa
changed in different trophic levels of the water column. For example, the
relative calcite contribution of the common placolith (i.e., <italic>G. oceanica</italic> and <italic>E. huxleyi</italic>) was higher in the water column with slightly
euphotic stations (e.g., stations with cyclonic eddy, shallow DCM, and
nutricline; Fig. 3). Their contribution decreased and the contribution of
<italic>F. profunda</italic> increased with the deepening of water depth, whereas the
contribution of other species remained constant (Fig. 7b). In contrast, these
placoliths contributed less in water columns with an oligotrophic station (e.g., stations with anticyclonic eddy, deep DCM, and nutricline; Fig. 3),
and an elevated contribution of other species was found in the upper <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 50 m of the water column (Fig. 7c). <italic>E. huxleyi</italic>, <italic>G. oceanica</italic>, and
<italic>F. profunda</italic> represented around half of the calcite in the water
column, whereas other species with smaller levels of abundance contribute to
the other 50 % of water-column calcite. The greater contribution of these
relatively less abundant species in calcite inventories is partly related to
higher per coccolith calcite contents, due in part to larger coccolith
lengths (Young and Ziveri, 2000); for example, <italic>O. fragilis</italic> has
&gt; 80 pg C per coccolith, whereas <italic>E. huxleyi</italic> has
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2 pg C per coccolith. Relatively rare coccolithophore species with
high coccolith and coccosphere calcite contents are important vectors of both
upper-ocean calcite production (Daniels et al., 2014) and deep-sea calcite
fluxes (Ziveri et al., 2007). However, an examination of sediment trap material
(500 m depth, 1500 m above the sea floor) in the northern SCS basin shows
that these three species (<italic>E. huxleyi</italic>, <italic>G. oceanica</italic>, and
<italic>F. profunda</italic>) dominating upper-ocean calcite inventories all have an
increased contribution to coccolith (&gt; 95 %) and coccolith
calcite (&gt; 80 %) fluxes (Fig. 7d, Jin et al., unpublished). The
significant loss of the calcite contribution from other species highlights
the discrepancy between coccolith calcite in the euphotic upper water column
and aphotic deep ocean. Notably, at 150 m for some stations (D9, F1, G2, I5,
X3), these three species can comprise more than 70 to 90 % of calcite
inventories and the contribution of <italic>G. oceanica</italic> exceeds that of
<italic>E. huxleyi</italic>, which is similar to the fluxes of sediments of moored
traps. One possible reason is that these coccoliths are attributed to lateral
transport of the nepheloid layer originating from the continental shelf or slope.
This is the most likely case for D9 and F1, as they have such high
detached coccolith concentrations (Fig. 6) and are located in the easternmost
part of the 18<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N section. Alternatively, coccoliths in the deep layer
are a result of vertical sinking. They can indicate that the higher
contribution of these species in the deep layer may result from their higher
production rate in the photic zone, which cannot be reflected by the
snapshot-like discrete sampling done in our study.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10" specific-use="star"><caption><p><bold>(a)</bold> Cell abundance (red triangles) and mean distal shield
length (DSL, blue dots; error bar: 1 SD) of <italic>E. huxleyi</italic> plotted
at stations where there were at least two biometry measurement points.
<bold>(b)</bold> A schematic map showing light and nutrient conditions in
relation to coccolithophore growth rate and cell or coccolith size.</p></caption>
          <?xmltex \igopts{width=483.69685pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f10.pdf"/>

        </fig>

</sec>
<sec id="Ch1.S4.SS4">
  <?xmltex \opttitle{Environmental influences on \textit{Emiliania huxleyi} biometry}?><title>Environmental influences on <italic>Emiliania huxleyi</italic> biometry</title>
      <p>Some parameters can describe coccolithophore calcification in field or
culturing studies. Firstly, coccolith biometry, which includes the parameters
of coccolith morphology such as shield length, thickness, and relative tube width (e.g., Poulton et al., 2011; Young and Ziveri, 2000; Young et al., 2014), is
directly associated with single-coccolith weight or calcite content. Our data
indicate that the biometry parameters of the <italic>E. huxleyi</italic> coccosphere,
i.e., CD, DSL, and N, are significantly correlated (results 3.4). The linear
relationship between DSL and CD (morphotype A cells) was also reported in
field (Triantaphyllou et al., 2010; Henderiks et al., 2012) and culture
samples (Bach et al., 2012; Müller et al., 2012) (Fig. 9a). As suggested
by Müller et al. (2012), it takes additional time for larger-sized cells
to transport coccoliths from vesicle to cell surface and hence more time for
coccolith maturation and formation so as to produce a larger-sized coccolith.
By multiplying single-coccolith weight by the number of coccoliths per coccosphere, we
get the cell calcite content, which mainly ranges from 10 to 70 pg for an
<italic>E. huxleyi</italic> type A cell in the SCS (Fig. 9b). The DSL / CD ratios for
<italic>E. huxleyi</italic> type A in the culturing and field samples are both within
their respective ranges, and the former is obviously higher than the latter
(Fig. 9a), which can be attributed to the fact that changes in a sole environmental
variant in sterile culture experiments can remarkably influence the
physiology of coccolith formation, whereas the effects on coccolith formation
can be muted due to the positive or negative responses to multiple
environmental changes in the field (Müller et al., 2012). With the same DSL,
coccosphere diameter in field samples is larger. It also seems that an <italic>E. huxleyi</italic> cell in the field can produce more or multilayer coccoliths, which could be a defense against zooplankton grazing or
bacterial attack and offer mechanical protection (Young, 1994; Jaya et al.,
2016) in natural conditions. As seen in Fig. 9b, the coccolith length
is likely to be able to reflect the morphology of a whole coccosphere and its
calcite content, i.e., the cellular particulate inorganic carbon (PIC)
content. And further, the linear relationship between the morphological
parameters makes it possible to reconstruct coccolithophore cell volume in
geological records (Henderiks, 2008).</p>
      <p>The second parameter is PIC production rate, i.e., the calcification rate, which
is calculated by the equation <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mtext>PIC</mml:mtext></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> growth rate
(<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">μ</mml:mi></mml:math></inline-formula>) <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> cellular PIC content in batch cultures (e.g., Langer et
al., 2006, 2009, 2012). Another is cell-specific calcite production (CP)
(e.g., Poulton et al., 2013, 2014; Charalampopoulou et al., 2011, 2016), which
is calculated by dividing CP by cell abundance. These two parameters are
obviously related to the cellular PIC content or single-coccolith calcite
content; however, they are not equivalent because both calcification rate and
cell-specific CP are also strongly influenced by coccolithophore or the coccolith
production rate. Hence, the following discussion is based on the coccolith
biometry-related parameters, e.g., coccolith or coccosphere length,
coccolith or coccosphere calcite content (weight).</p>
<sec id="Ch1.S4.SS4.SSS1">
  <title>Nutrient and light</title>
      <p>The statistically significant correlation between the nutrient and mean DSL
of <italic>E. huxleyi</italic> suggests that both nitrogen and phosphorus exert a positive
influence on coccolith length. However, in nutrient-limited batch cultures,
it has been shown that <italic>E. huxleyi</italic> morphology displayed divergent
responses to different types of resource limitation; e.g., coccolith or
coccosphere length or volume and/or calcite content deceased and increased
under nitrogen- and phosphorus-limited conditions, respectively (Riegman et
al., 2000; Müller et al., 2008, 2012; Oviedo et al., 2014). The increased
coccolith or coccosphere size of <italic>E. huxleyi</italic> was also found in
phosphorus-deficient mesocosm enclosures (Båtvik et al., 1997; Engel et
al., 2005). The interpretation is that nitrogen and phosphorus are required
for distinctly different cellular uses: nitrogen for biomass growth and
phosphorus for cell division and organic maturity (e.g., Arrigo, 2005;
Aloisi, 2015). Therefore, under nitrogen limitation, coccolithophores will
produce smaller cells with a smaller-sized coccolith, and on the other hand,
phosphorus limitation inhibits cell division, whereas biomass in cells still
grows, leading to an increase in coccolith or coccosphere size (Müller et
al., 2008, 2012). Back to the present case, the nutrient limitation theory
indicates that nitrogen should be the main controlling factor on coccolith
size. The positive relation of DSL and phosphorus may come from the high
intercorrelation between the two types of nutrients (Pearson, <inline-formula><mml:math display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.99,
<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F11"><caption><p><italic>E. huxleyi</italic> type A distal shield length (DSL) in the South
China Sea (black circles) with those in neritic populations (hollow diamonds) and
oceanic populations (hollow triangles) in the North Sea (Young et al., 2014), plotted versus
carbonate calcium saturation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>.</p></caption>
            <?xmltex \igopts{width=184.942913pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4843/2016/bg-13-4843-2016-f11.pdf"/>

          </fig>

      <p>Nutrient is an important limiting factor in <italic>E. huxleyi</italic> growth (i.e.,
under laboratory culturing conditions); when nutrients are replete, <italic> E. huxleyi</italic> growth is fast (exponential phase), with fewer and smaller
coccoliths per cell. When nutrients become limiting, <italic>E. huxleyi</italic>
growth slows (stationary phase), and larger and multilayer coccospheres are
produced (Gibbs et al., 2013). Besides nutrients, it is suggested that light
should also be a limiting factor for <italic>E. huxleyi</italic> production and
calcification in natural community (e.g., Poulton et al., 2007, 2010, 2014;
Charalampopoulou et al., 2011). With a closer inspection of the DSL data, the
largest coccoliths occurred at the deepest depths where nutrients were sufficient and light was insufficient, while within the <italic>E. huxleyi</italic>
abundant depth coccoliths were relatively small (most remarkable at X3, F1,
D9, I7, X5; Fig. 10a). Estimated from the monthly (June 2014) instantaneous
PAR (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2000 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math 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 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>, ocean color Aqua-MODIS
satellite) in the SCS, the PAR in the water column was about 200, &lt; 100, and
20 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math 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 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 50 (10 %), 75
(&lt; 5 %), and 100 m (1 %) depth, respectively. <italic>E. huxleyi </italic>growth is likely to be limited by light, although some authors have
stated that light should not be regarded as a factor regulating phytoplankton
growth in the oligotrophic SCS as the euphotic zone depth exceeds the MLD and
nutricline throughout the year (Tseng et al., 2005; Wong et al., 2007). The
higher half-saturation constants of <italic>E. huxleyi</italic> for light
(<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 100 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math 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 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 <italic>E. huxleyi</italic> and
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math 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 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 other phytoplankton groups; Tyrrell and Taylor, 1996) may support our statement that <italic>E. huxleyi</italic>
growth is more light-dependent in the SCS. Here, we propose a simple
schematic (Fig. 10b). (1) In the DCM layer, where light and nutrients are
optimal for phytoplankton growth, <italic>E. huxleyi</italic> growth is fast and the species produces small-sized coccoliths. (2) In deeper waters, when nutrients are more
sufficient but light is not available, <italic>E. huxleyi</italic> growth slows and
the species produces larger-sized coccoliths. It has been reported that an <italic>E. huxleyi</italic> cell can produce higher-calcite-content coccoliths with a lower growth
rate in light-limited continuous cultures (Fritz and Balch, 1996; Fritz,
1999). That light limitation, in <italic>E. huxleyi</italic> cells, can prolong the G1
assimilation stage during which calcification takes place and will eventually increase cellular calcite content (Müller et al., 2008). Although
coccolith formation is a light-dependent process, it does not seem to be
impeded in the low-light conditions. This could be owing to the calcification having a lower light-saturated threshold than photosynthesis
(Müller et al., 2008). (3) Above the nutricline, where light intensity is
high and multi-nutrients are depleted, it is possible that <italic>E. huxleyi</italic> coccolith size is dependent on whether inorganic phosphorus is
deficient or organic phosphorus compounds can be utilized, although we lack
data to directly address either nutrient availability or coccolith biometry
in these samples.</p>
</sec>
<sec id="Ch1.S4.SS4.SSS2">
  <title>Temperature</title>
      <p>Temperature is expected to be a critical factor for coccolithophore growth and cell
size. An <italic>E. huxleyi</italic> strain isolated from Great Barrier Reef showed
an optimal growth temperature at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C with the smallest cell size,
while the growth rate and cell size became lower and bigger in parallel as the
temperature was decreased to 10 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (Sorrosa et al., 2005). A recent
culturing study (Saruwatari et al., 2016) has also shown that <italic>E. huxleyi</italic> strains of the morphotype B/C isolated from the Arctic Ocean grow faster
and produce smaller coccoliths when temperature increases from 5 to
20 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. However, contradictory results come from Rosas-Navarro et
al. (2016), who have found that <italic>E. huxleyi</italic> (type A, strains isolated
from North Pacific Ocean) produces the largest coccoliths within the optimal
growth temperature of 20 to 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. Apparently, these different
patterns of <italic>E. huxleyi</italic> coccolith size may result from
strain-specific or morphotype (ecotype) responses to temperature. In the
present study, temperature was not found to correlate with <italic>E. huxleyi</italic> coccolith size from the statistical analysis (Table 3). One possible
reason could be that the temperature profiles were to a large extent controlled
by the eddy-related water-column structure (i.e., MLD), which may possibly
mute the signal of their influences on <italic>E. huxleyi</italic> growth and size.
Alternatively, as stated by Bach et al. (2012), temperature may exert little
physiological influence on <italic>E. huxleyi</italic> size. In addition, the
temperature at the investigated stations ranged from 18 to 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C at
depths from 100 to 50 m, which is near the optimal growth temperature for
many <italic>E. huxleyi</italic> strains (20 to 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C; Paasche, 2002;
Sorrosa et al., 2005; Rosas-Navarro et al., 2016). That is, temperature may
not be a limiting factor for <italic>E. huxleyi</italic> growth within the euphotic
zone in the tropical SCS, apart from surface and/or near-surface waters where
water temperatures are &gt; 29 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, above the growth optimum
temperature range for this species (Rosas-Navarro et al., 2016).</p>
</sec>
<sec id="Ch1.S4.SS4.SSS3">
  <title>Carbonate chemistry</title>
      <p>Coccolithophores are thought to be sensitive indicators of carbonate
chemistry, especially <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and [CO<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>] (e.g., Beaufort
et al., 2011). Our results show that the mean DSL is inversely correlated
with pH and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Indeed, all the environmental data were
significantly intercorrelated (Table 3), nearly all contributing to one
principal component (PC-1, 76.59 % of variance) (Table 3). That is, the
environmental gradients in the water column are dependent on sampling depth.
Importantly, in the data from the SCS the carbonate chemistry inversely
mirrors the nutrient data, making it hard to distinguish its influence on
coccolith morphology. Similarly, due to the high intercorrelation levels of
all environmental variants in two transects in the Southern Ocean, carbonate
chemistry does not seem to be the best interpretation for <italic>E. huxleyi</italic>
cell-specific calcification (Charalampopoulou et al., 2016). Hence, it is not
possible to directly infer that <italic>E. huxleyi</italic> coccolith size and
carbonate chemistry have a simple cause and effect relationship in the SCS.</p>
      <p>Here, our DSL results in the SCS were compared with those in the North Sea
(Young et al., 2014) (Fig. 11). In the North Sea, <italic>E. huxleyi</italic> was
also dominated by morphotype A (Young et al., 2014). While
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in the two regions falls within a similar range, DSL
shows a significant difference (<inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 17.18, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01). Young
et al. (2014) have argued that <italic>E. huxleyi</italic> DSL differences relate to
neritic and oceanic groups rather than to carbonate chemistry impacts. DSLs in
our samples show no significant difference with those in the oceanic group
(<inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.243, <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.63); however, they are significantly lower than
those in the neritic group from Young et al. (2014) (<inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 125.2, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01) (Fig. 11). Hence, what causes the morphological distinction
may be genotypic variation or an <italic>ecological</italic> effect (Bach et al.,
2012). It is suggested that the changing environmental conditions can select
for different coccolithophore strains, which indirectly influences the
coccolith size and morphology (Bach et al., 2012). For example, different
environmental provinces can shift from a community dominated by normally
calcified <italic>E. huxleyi</italic> type A to one characterized by weakly calcified
B/C on the Patagonian Shelf and in the Southern Ocean (Cubillos et al., 2007;
Poulton et al., 2011). More heavily calcified morphotypes during low
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in winter may be responsible for the seasonal morphotype
transition in the Bay of Biscay (Smith et al., 2012). Seasonal variability of
<italic>E. huxleyi</italic> coccolith size has also been observed in the Aegean Sea,
which may be due to genotypic or ecophenotypic variation (Triantaphyllou et
al., 2010). Meier et al. (2014) found that mean coccolith weight peaked at
the Rockall Plateau during Heinrich event 11, when <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and pH
had minimum values. This could be due to a coccolith assemblage shift to
more heavily calcified morphotypes in relation to oceanic frontal changes during
this geological episode rather than the influences of carbonate chemistry
(Meier et al., 2014). In conclusion, the ecological transition of assemblages
may have a more dominant effect on coccolith morphology and/or cellular
calcification not only in the present ocean but also in geological records.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions</title>
      <p>In the South China Sea (SCS), the coccolithophore community corresponds to
the tropical biogeographic zone, with many characteristic tropical species
being present (e.g., <italic>Umbellosphaera irregularis</italic>,
<italic>Florisphaera profunda</italic>). Coccolithophore cellular abundances ranged
from &lt; 0.27 cells mL<inline-formula><mml:math 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> to 83.67 cells mL<inline-formula><mml:math 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> across the
SCS basin. Highest cell concentrations occurred in the deep chlorophyll
maximum, with all of the coccolithophore community within the euphotic zone
(i.e., above the depth where 1 % of surface irradiance penetrates).
<italic>Emiliania huxleyi</italic> (type A) was the numerically dominant species in
the SCS during summer.</p>
      <p>Water samples were divided into three groups according to the composition of
their coccolithophore communities. Group 1, characterized by the presence of
<italic>U. irregularis</italic>, preferred oligotrophic conditions; Group 2,
dominated by <italic>E. huxleyi</italic>, had relative high coccolithophore cell
abundances; and Group 3 contained lower photic species such as <italic>F. profunda</italic>. These coccolithophore communities through the water column showed
strong vertical differentiation, with depth shifts in response to mesoscale
eddy features along the 18<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N section (Figs. 5, 8). Briefly,
anticyclonic eddies were occupied with oligotrophic representative species,
whereas coccolithophore assemblages in the cyclonic eddy were slightly
productive.</p>
      <p>Estimates of calcite concentrations in the upper water column based on
coccosphere and coccolith calcite contents closely matched detached coccolith
concentrations, highlighting their significant contribution to calcite
standing stocks. Three key species (<italic>E. huxleyi</italic>, <italic>Gephyrocapsa oceanica</italic>, <italic>F. profunda</italic>) contributed roughly half (Fig. 7) of the
surface ocean coccolith-calcite concentrations. Moreover, they had an
increased contribution to deep-sea coccolith and calcite fluxes (Jin et al.,
unpublished), highlighting their importance for coccolith carbonate production in
the SCS.</p>
      <p>Biometric measurements of <italic>E. huxleyi</italic> coccoliths showed significant
(<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mi mathvariant="italic">&lt;</mml:mi></mml:mrow></mml:math></inline-formula> 0.01) positive relationships with nutrient (nitrate,
phosphate) concentrations and negative relationships with carbonate chemistry
(pH, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Ω</mml:mi><mml:mi mathvariant="normal">C</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Table 3), although all of these environmental
parameters were strongly correlated. It is suggested that light and nutrients
are more likely to explain the <italic>E. huxleyi</italic> coccolith variations
rather than carbonate chemistry. Larger-sized coccoliths for <italic>E. huxleyi</italic> are produced in deep and light-limited waters with a slow cell growth
rate, while in optimal conditions (i.e., in deep chlorophyll maximum), they
are likely to produce smaller-sized coccoliths with faster growth rates.</p>
</sec>

      
      </body>
    <back><app-group>
        <supplementary-material position="anchor"><p><bold>The Supplement related to this article is available online at <inline-supplementary-material xlink:href="http://dx.doi.org/10.5194/bg-13-4843-2016-supplement" xlink:title="pdf">doi:10.5194/bg-13-4843-2016-supplement</inline-supplementary-material>.</bold></p></supplementary-material>
        </app-group><notes notes-type="authorcontribution">

      <p>Xiaobo Jin, Chuanlian Liu, and Alex J. Poulton designed the experiments and
Xiaobo Jin carried them out. Chuanlian Liu was the supervisor of this
project. Xiaobo Jin and Alex J. Poulton drafted and revised the manuscript.
Nutrients and carbonate chemistry data were provided by Minhan Dai and
Xianghui Guo.</p>
  </notes><ack><title>Acknowledgements</title><p>This work is financed by the National Natural Science Foundation of China
(grant nos. 91228204, 41376047). We are grateful to the cruise colleagues of
R/V <italic>Dongfanghong II</italic> and the Ocean Carbon Group of Xiamen University.
We are also grateful to R. B. Pearce, R. M. Sheward, and G. M. Fragoso for
their assistance in light and scanning electron microscopy and to H. E. K. Smith for her assistance in statistical analysis (National
Oceanography Centre). M. Wang and H. R. Zhang are thanked for their
assistance in AVISO data compiling. A. J. Poulton would also like to
acknowledge financial support from National Capability funding from the
Natural Environmental Research Council. We also thank the anonymous reviewers
for their constructive comments on the discussion paper. <?xmltex \hack{\newline}?><?xmltex \hack{\newline}?> Edited by: K. Suzuki<?xmltex \hack{\newline}?> Reviewed by: two
anonymous referees</p></ack><ref-list>
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    <!--<article-title-html>Coccolithophore responses to environmental variability in the South China
Sea: species composition and calcite content</article-title-html>
<abstract-html><p class="p">Coccolithophore contributions to the global marine carbon cycle are regulated
by the calcite content of their scales (coccoliths) and the relative cellular
levels of photosynthesis and calcification rates. All three of these factors
vary between coccolithophore species and with response to the growth
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South China Sea (SCS) during summer 2014 in order to examine how
environmental variability influenced species composition and cellular levels
of calcite content. Average coccolithophore abundance and their calcite
concentration in the water column were 11.82 cells mL<sup>−1</sup> and
1508.3 pg C mL<sup>−1</sup>, respectively, during the cruise. Water samples can
be divided into three floral groups according to their distinct
coccolithophore communities. The vertical structure of the coccolithophore
community in the water column was controlled by the trophic conditions, which
were regulated by mesoscale eddies across the SCS basin. The evaluation of
coccolithophore-based calcite in the surface ocean also showed that three key
species in the SCS (<i>Emiliania huxleyi</i>, <i>Gephyrocapsa
oceanica</i>, <i>Florisphaera profunda</i>) and other larger, numerically rare
species made almost equal contributions to total coccolith-based calcite in
the water column. For <i>Emiliania huxleyi</i> biometry measurements,
coccolith size positively correlated with nutrients (nitrate, phosphate), and
it is suggested that coccolith length is influenced by light and nutrients
through the regulation of growth rates. Larger-sized coccoliths were also
linked statistically to low pH and calcite saturation states; however, it is
not a simple cause and effect relationship, as carbonate chemistry was
strongly co-correlated with the other key environmental factors (nutrients,
light).</p></abstract-html>
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