<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing with OASIS Tables v3.0 20080202//EN" "journalpub-oasis3.dtd">
<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">
  <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-13-2715-2016</article-id><title-group><article-title>Effect of light on photosynthetic efficiency of sequestered chloroplasts in
intertidal benthic foraminifera <?xmltex \hack{\newline}?>(<italic>Haynesina germanica</italic> and <italic>Ammonia tepida</italic>)</article-title>
      </title-group><?xmltex \runningtitle{Effect of light on photosynthetic efficiency of sequestered chloroplasts}?><?xmltex \runningauthor{T.~Jauffrais et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1 aff5">
          <name><surname>Jauffrais</surname><given-names>Thierry</given-names></name>
          <email>thierry.jauffrais@univ-angers.fr</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2 aff3 aff5">
          <name><surname>Jesus</surname><given-names>Bruno</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Metzger</surname><given-names>Edouard</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Mouget</surname><given-names>Jean-Luc</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Jorissen</surname><given-names>Frans</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Geslin</surname><given-names>Emmanuelle</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et
Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX
1, France</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>EA2160, Laboratoire Mer Molécules Santé, 2 rue de
la Houssinière, Université de Nantes, 44322 Nantes CEDEX 3,
France</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>BioISI – Biosystems &amp; Integrative Sciences Institute,
Campo Grande University of Lisboa, Faculty of Sciences, 1749-016 Lisboa,
Portugal</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>EA2160, Laboratoire Mer Molécules Santé,
Université du Maine, Ave O. Messiaen, 72085 Le Mans CEDEX 9,
France</institution>
        </aff>
        <aff id="aff5"><label>*</label><institution>These authors contributed equally to this work.</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Thierry Jauffrais (thierry.jauffrais@univ-angers.fr)</corresp></author-notes><pub-date><day>10</day><month>May</month><year>2016</year></pub-date>
      
      <volume>13</volume>
      <issue>9</issue>
      <fpage>2715</fpage><lpage>2726</lpage>
      <history>
        <date date-type="received"><day>21</day><month>December</month><year>2015</year></date>
           <date date-type="rev-request"><day>18</day><month>January</month><year>2016</year></date>
           <date date-type="rev-recd"><day>22</day><month>April</month><year>2016</year></date>
           <date date-type="accepted"><day>25</day><month>April</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/13/2715/2016/bg-13-2715-2016.html">This article is available from https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016.html</self-uri>
<self-uri xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016.pdf</self-uri>


      <abstract>
    <p>Some benthic foraminifera have the ability to incorporate functional
chloroplasts from diatoms (kleptoplasty). Our objective was to investigate
chloroplast functionality of two benthic foraminifera (<italic>Haynesina germanica</italic> and <italic>Ammonia tepida</italic>) exposed to
different irradiance levels (0, 25, 70 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photon 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: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>
using spectral reflectance, epifluorescence observations, oxygen evolution
and pulse amplitude modulated (PAM) fluorometry (maximum photosystem II
quantum efficiency (Fv/Fm) and rapid light curves (RLC)). Our results clearly
showed that <italic>H. germanica</italic> was capable of using its kleptoplasts for more than 1 week
while <italic>A. tepida</italic> showed very limited kleptoplastic ability with  maximum photosystem II
quantum efficiency (Fv/Fm <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.4), much lower than <italic>H. germanica</italic> and decreasing to zero in only
1 day. Only <italic>H. germanica</italic> showed net oxygen production with a compensation point at 24 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photon 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>
and a production up to 1000 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> day<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 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photon 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>.
<italic>Haynesina germanica</italic> Fv/Fm slowly decreased from 0.65 to 0.55 in 7 days when kept in darkness;
however, it quickly decreased to 0.2 under high light. Kleptoplast
functional time was thus estimated between 11 and 21 days in darkness and
between 7 and 8 days at high light. These results emphasize that studies
about foraminifera kleptoplasty must take into account light history.
Additionally, this study showed that the kleptoplasts are unlikely to be
completely functional, thus requiring continuous chloroplast resupply from
foraminifera food source. The advantages of keeping functional chloroplasts
are discussed but more information is needed to better understand
foraminifera feeding strategies.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>Benthic foraminifera colonize a wide variety of sediments from brackish
waters to deep-sea environments and can be the dominant meiofauna in these
ecosystems (Gooday, 1986; Pascal et al., 2009). They may play a relevant role
in the carbon cycle in sediments from deep sea
(Moodley et al., 2002) to brackish environments
(Thibault de Chanvalon et al., 2015). Their minor role in organic carbon
cycling in aerobic sediments, compared to bacteria, contrasts with their
strong contribution to anaerobic organic matter mineralisation
(Geslin et al., 2011) and they can be responsible for
up to 80 % of benthic denitrification (Pina-Ochoa et al., 2010;
Risgaard-Petersen et al., 2006).</p>
      <p>Some benthic foraminiferal species are known to sequester chloroplasts from
their food source and store them in their cytoplasm   (Lopez,
1979; Bernhard and Bowser, 1999) in a process known as kleptoplasty (Clark
et al., 1990). A kleptoplast is thus a chloroplast, functional or
not, that was “stolen” and integrated by an organism. Kleptoplastic
foraminifera are found in intertidal sediments (e.g. <italic>Haynesina</italic>, <italic>Elphidium</italic> and <italic>Xiphophaga</italic>)
(Lopez, 1979; Correia and Lee, 2000, 2002a, b; Goldstein et al., 2010; Pillet et al., 2011),
low oxygenated aphotic environments (<italic>Nonionella, Nonionellina, Stainforthia</italic>)  (Bernhard and Bowser, 1999; Grzymski
et al., 2002) and shallow-water sediments (<italic>Bulimina elegantissima</italic>)  (Bernhard and
Bowser, 1999). The role of chloroplasts sequestered by benthic foraminifera
is poorly known and photosynthetic functions have only been studied in a few
mudflat species (<italic>Elphidium williamsoni</italic>, <italic>Elphidium excavatum</italic> and <italic> Haynesina germanica</italic>)
(Lopez, 1979; Correia and Lee, 2000, 2002a, b; F. Cesbron, personal communication, 2015).
Amongst the deep-sea benthic foraminifer living in the
aphotic zone, only <italic>Nonionella stella</italic> has been studied  (Grzymski et al., 2002). The
authors suggest that the sequestered chloroplasts in this species may play a
role in the assimilation of inorganic nitrogen, even when light is absent.
It has also been hypothesised that chloroplast retention may play a major
role in foraminiferal survival when facing starvation periods or in anoxic
environments (F. Cesbron, personal communication, 2015). Under these conditions, kleptoplasts
could potentially be used as a carbohydrate source, and participate in
inorganic nitrogen assimilation (Falkowski and Raven, 2007) or, when
exposed to light, to produce oxygen needed in foraminiferal aerobic
respiration  (Lopez, 1979).</p>
      <p>Foraminifera pigment and plastid ultrastructure studies have shown that the
chloroplasts are sequestered from their food source, i.e. mainly from
diatoms (Lopez, 1979; Knight and Mantoura, 1985; Grzymski et al., 2002;
Goldstein, 2004). This was confirmed by experimental feeding studies
(Correia and Lee, 2002a; Austin et al., 2005) and by molecular analysis of
kleptoplastic foraminifera from different environments  (Pillet et al.,
2011; Tsuchiya et al., 2015). Foraminifera from intertidal mudflat
environments (e.g. <italic>H. germanica</italic>, <italic> A. tepida</italic>) feed mostly on pennate diatoms  (Pillet et
al., 2011) which are the dominant microalgae in intertidal mudflat sediments
(MacIntyre et al., 1996; Jesus et al., 2009). Furthermore, in these
transitional coastal environments (e.g. estuaries, bays, lagoons) <italic>A. tepida</italic> and <italic>H. germanica</italic> are
usually the dominant meiofauna species in West Atlantic French coast
mudflats (Debenay et al., 2000, 2006; Morvan et al., 2006; Bouchet et al.,
2009; Pascal et al., 2009; Thibault de Chanvalon et al., 2015). Their vertical
distribution in the sediment is characterised by a clear maximum density at
the surface (Alve and Murray, 2001; Bouchet et al., 2009; Thibault de
Chanvalon et al., 2015) with access to light, followed by a sharp decrease in
the next two centimetres (Thibault de Chanvalon et al., 2015).</p>
      <p>Foraminiferal kleptoplast retention times can vary from days to months
(Lopez, 1979; Lee et al., 1988; Correia and Lee, 2002b; Grzymski et al., 2002).
The source of this variation is poorly known but longer kleptoplast
retention times were found in dark treatments  (Lopez, 1979; Correia
and Lee, 2002b), thus suggesting an effect of light exposure, similar to what
is observed in kleptoplastic sacoglossans   (Trench et al., 1972; Clark et
al., 1990; Evertsen et al., 2007; Vieira et al., 2009), possibly related to the
absence of some components of the kleptoplast photosynthetic protein
complexes in the host (Eberhard et al., 2008).</p>
      <p>Most recent studies on kleptoplastic foraminifera focused on feeding,
genetics and microscopic observation related to chloroplast acquisition
(e.g., Austin et al., 2005; Pillet et al., 2011; Pillet and Pawlowski, 2013).
To our knowledge little is known about the effects of abiotic factors on
photosynthetic efficiency of sequestered chloroplasts in benthic
foraminifera, particularly on the effect of light intensity on kleptoplast
functionality. Non-invasive techniques are ideal to follow photosynthesis
and some have already been used to study foraminifera respiration and
photosynthesis, e.g. oxygen evolution by microelectrodes (Rink et al., 1998;
Geslin et al., 2011) or <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>14</mml:mn></mml:msup></mml:math></inline-formula>C radiotracer  (Lopez, 1979). Recently,
pulse amplitude modulated (PAM) fluorometry has been used extensively in the
study of kleptoplastic sacoglossans  (Vieira et al., 2009; Costa et al., 2012;
Jesus et al., 2010; Serodio et al., 2010; Curtis et al., 2013; Ventura et
al.,
2013). This non-invasive technique has the advantage of estimating relative
electron transport rates (rETR) using rapid light curves (RLC) and
photosystem II (PSII) maximum quantum efficiencies (Fv/Fm) very quickly and
without incubation periods. The latter parameter has been shown to be a good
parameter to estimate PSII functionality (e.g. Vieira et al., 2009; Jesus et
al., 2010; Serodio et al., 2010; Costa et al., 2012; Curtis et al., 2013;
Ventura et al., 2013).</p>
      <p>The objective of the current work was to investigate the effect of
irradiance levels on photosynthetic efficiency and chloroplast functional
times of two benthic foraminifera feeding in the same brackish areas, <italic>H. germanica</italic>,
which is   known to sequester chloroplasts   and <italic>A. tepida</italic>, not   known to sequester
chloroplasts. These two species were exposed to different irradiance levels
during 1 week and chloroplast efficiency was measured using
epifluorescence, oxygen microsensors and PAM fluorometry.</p>
</sec>
<sec id="Ch1.S2">
  <title>Materials and methods</title>
<sec id="Ch1.S2.SS1">
  <title>Sampling</title>
      <p><italic>Haynesina germanica</italic> and <italic>A. tepida</italic> were sampled in January 2015 in Bourgneuf
Bay (47.013<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 2.019<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W), a coastal bay with a large mudflat situated south of
the Loire estuary on the French west coast. In this area, all specimens of
<italic>A. tepida</italic> belong to genotype T6 of Hayward et al. (2004) (M. Schweizer, personal communication, 2015). In
the field, a large amount (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 20 kg) of the upper sediment
layer (roughly first 5 mm) was sampled and sieved over 300 and 150 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m
meshes using in situ sea water. The 150 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m fraction was collected in dark
flasks and maintained overnight in the dark at 18 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in the
laboratory. No additional food was added. In the following day, sediment
with foraminifera was diluted with filtered (GF/C, 1.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m, Whatman)
autoclaved sea-water (temperature: 18 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C and salinity: 32) and <italic>H. germanica</italic>
and <italic>A. tepida</italic> in healthy conditions (i.e. with cytoplasm inside the test) were
collected with a brush using a stereomicroscope (Leica MZ 12.5). The
selected specimens were rinsed several times using Bourgneuf bay
filtered-autoclaved seawater to minimize bacterial and microalgal
contamination.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Size and biovolume determination</title>
      <p>Foraminifera test mean maximal elongation (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m, the length of the axes
going from the last chamber to the other side of the test and passing by the
umbilicus) was measured using a micrometre mounted on a Leica
stereomicroscope (MZ 12.5). Mean foraminiferal volume was approximated with
the equation of a half sphere, which is the best resembling geometric shape
for <italic>H. germanica </italic>and <italic>A. tepida</italic> (Geslin et al., 2011). The cytoplasmic volume (or biovolume) was
then estimated by assuming that the internal test volume corresponds to
75 % of the total foraminiferal test volume (Hannah et al., 1994).</p>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Spectral reflectance</title>
      <p>Pigment spectral reflectance was measured non-invasively to determine and
compare the relative pigment composition on 50 fresh specimens of <italic>H. germanica</italic>, on 50
fresh specimens of <italic>A. tepida</italic> and on a benthic diatom as explained in Jesus et al. (2008).
Concisely, a USB2000 (Ocean Optics, Dunedin, FL, USA)
spectroradiometer with a VIS-NIR optical configuration controlled by
OObase32 software (Ocean Optics B.V., Duiven, the Netherlands) was used. The
spectroradiometer sensor was positioned so that the surface was always
viewed from the nadir position. Foraminiferal reflectance spectra were
calculated by dividing the upwelling spectral radiance from the foraminifera
(Lu) by the reflectance of a clean polystyrene plate (Ld) for both of which
the machine dark noise (Dn) was subtracted (Eq. 1).
            <disp-formula id="Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mo>(</mml:mo><mml:mtext>Lu</mml:mtext><mml:mo>-</mml:mo><mml:mtext>Dn</mml:mtext><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mo>(</mml:mo><mml:mtext>Ld</mml:mtext><mml:mo>-</mml:mo><mml:mtext>Dn</mml:mtext><mml:mo>)</mml:mo></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:math></disp-formula></p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Image analysis</title>
      <p>Foraminifera   kleptoplast fluorescence was measured using epifluorescence
microscopy (<inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 200, Olympus Ax70 with Olympus U-RFL-T, excitation
wave length 485 nm). Two Tif images (1232 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 964 px) of each
foraminifer were taken (one bright field photography and one epifluorescence
photography) using LUCIA G<sup>™</sup> software. The bright field photography was
used to trace the contours of the foraminifer and an ImageJ macro was used
to extract the mean pixel values of the corresponding epifluorescence
photography. Higher mean pixel values corresponded to foraminifera emitting
more fluorescence and thus, as a proxy, contain more chlorophyll. In an RGB
image each channel contains pixels between 0 and 255 values. The majority of
the information regarding chlorophyll fluorescence is encoded in the red
channel, therefore the green and blue channel were discarded and only the
red channel was kept. The images from the different treatments were directly
comparable as all images were taken using the same acquisition settings.
Thus, the mean red pixel values were used as a proxy for chlorophyll
fluorescence.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <title>Oxygen measurements</title>
      <p>Oxygen was measured using advanced Clark type oxygen microelectrodes of 50 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m
in diameter  (Revsbech, 1989) (OXI50 – Unisense, Denmark).
Electrodes were calibrated with a solution of sodium ascorbate at 0.1 M
(0 %) and with seawater saturated with oxygen by bubbling air (100 %).
Foraminiferal photosynthesis and oxygen respiration rates were measured
following Høgslund et al. (2008) and Geslin et
al. (2011). Measurements were carried out in a
micro-tube made from glass Pasteur pipette tips with an inner diameter of 1 mm.
The micro-tube was fixed to a small vial, filled with filtered
autoclaved seawater from Bourgneuf Bay. The vial was placed in an aquarium
with water kept at room temperature (18 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). A small brush was
used to position a pool of 7 to 10 foraminifera in the glass micro-tube
after removing air bubbles. Oxygen micro-profiles started at a distance of
200 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m above the foraminifers to avoid oxygen turbulences often
observed around the foraminifers. Measurements were registered when the
oxygen micro-profiles were stable; they were then repeated five time in the
centre of the micro-tube, using 50 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m steps until 1000 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m away
from the foraminifers (Geslin et al., 2011). The oxygen
flux (<inline-formula><mml:math display="inline"><mml:mi>J</mml:mi></mml:math></inline-formula>) was calculated using the first law of Fick:
            <disp-formula id="Ch1.E2" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>J</mml:mi><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mi>D</mml:mi><mml:mo>×</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mtext>d</mml:mtext><mml:mi>C</mml:mi></mml:mrow><mml:mrow><mml:mtext>d</mml:mtext><mml:mi>x</mml:mi></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math display="inline"><mml:mi>D</mml:mi></mml:math></inline-formula> is the oxygen diffusion coefficient (cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> s<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
experimental temperature (18 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) and salinity
(32) (Li and Gregory, 1974), and d<inline-formula><mml:math display="inline"><mml:mi>C</mml:mi></mml:math></inline-formula>/d<inline-formula><mml:math display="inline"><mml:mi>x</mml:mi></mml:math></inline-formula> is the oxygen concentration
gradient (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cm<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>. The O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> concentration gradients were
calculated with the oxygen profiles and using the <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:mrow></mml:math></inline-formula> of the
regression line to determine the best gradient. Total O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> consumption
and production rates were calculated as the product of O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes by the
surface area of the micro-tube and subsequently divided by the foraminifera
number to finally obtain the cell specific rate (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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>
(Geslin et al., 2011).</p>
</sec>
<sec id="Ch1.S2.SS6">
  <title>Fluorescence</title>
      <p>All pulse amplitude modulated fluorescence measurements were carried out
with a Water PAM fluorometer (Walz, Germany) using a blue measuring light.
Chloroplast functionality was estimated by monitoring PSII maximum quantum
efficiency (Fv/Fm) and by using <inline-formula><mml:math display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>-<inline-formula><mml:math display="inline"><mml:mi>I</mml:mi></mml:math></inline-formula> rapid light curve (RLC, e.g., Perkins et al., 2006)
parameters (<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, initial slope of the RLC at limiting
irradiance; rETRmax, maximum relative electron transport rate; Ek, light
saturation coefficient; and Eopt, optimum light) (Platt et al.,
1980). Rapid light curves were constructed using eight
incremental light steps (0, 4, 15, 20, 36, 48, 64, 90 and 128 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>,
each lasting 30 s. The PAM probe was set
up on a stand holder at a 2 mm distance from a group of 10 foraminifera.</p>
</sec>
<sec id="Ch1.S2.SS7">
  <title>Experimental design</title>
      <p><italic>Haynesina germanica</italic>, a species   known to sequester chloroplasts, were placed in plastic Petri
dishes and starved for 7 days under three different light conditions:
dark (D and Dark-RLC), low light (LL, 25 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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 high light (HL, 70 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>;
whereas  for comparison, <italic>A. tepida</italic>, a foraminifer  not known to sequester chloroplasts was
starved but only exposed to the dark condition. A short-term experiment was
thus carried out (7 days) to study the effect of light on healthy specimens
rather than the effect of starvation. For each condition, 10 specimens were
used per replicate and three replicates per light treatment; furthermore all
plastic Petri dishes were filled with Bourgneuf bay filtered-autoclaved
seawater. This experiment was carried out in a thermo-regulated culture room
at 18 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, equipped with cool light fluorescent lamp (Lumix day
light, L30W/865, Osram) and using a 14:10 h
(Light : Dark) photoperiod. The
distances between the light and the experimental conditions were assessed
using a light-metre and a quantum sensor (ULM-500 and MQS-B of Walz) to
obtain the desirable light intensities. Concerning the dark condition, the
Petri dishes were placed in a box covered with aluminium foil.</p>
      <p><italic>Haynesina germanica</italic> kleptoplast fluorescence was measured using epifluorescence microscopy, as
explained above, before and after the different light treatments. At the
beginning of the experiment it was done on 30 independent specimens to
assess the natural and initial variation of <italic>Haynesina germanica </italic>kleptoplast fluorescence. At the
end of the experiment, the measurements were done on all foraminifera exposed
to the different light conditions (a total of 30 specimens per condition).
This was also measured on <italic>A. tepida</italic>, but results are not presented because no
chlorophyll fluorescence was observed at the end of the experiment.</p>
      <p><italic>Haynesina germanica</italic> and <italic>A. tepida</italic> oxygen production and consumption were measured at the beginning of
the experiment on three independent replicates with seven specimens in each
replicate. Six different light steps were used to measure O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> production
(0, 25, 50, 100, 200 and 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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> for <italic>H. germanica</italic> and
only two light steps (0 and 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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> for <italic>A. tepida</italic>.
Photosynthetic activity (<inline-formula><mml:math display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>) data of <italic>H. germanica</italic> were fitted with a Haldane model, as
modified by Papacek et al. (2010) and Marchetti et al. (2013) but without
photoinhibition (Eq. 3).
            <disp-formula id="Ch1.E3" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>P</mml:mi><mml:mo>(</mml:mo><mml:mi>I</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mtext>Pm</mml:mtext><mml:mo>×</mml:mo><mml:mi>I</mml:mi></mml:mrow><mml:mrow><mml:mi>I</mml:mi><mml:mo>+</mml:mo><mml:mtext>Ek</mml:mtext></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>-</mml:mo><mml:mtext>Rd</mml:mtext><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where Pm is the maximum photosynthetic capacity (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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>,
<inline-formula><mml:math display="inline"><mml:mi>I</mml:mi></mml:math></inline-formula> the photon flux density (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>,
Ek the half-saturation constant (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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 Rd
the dark respiration, expressed as an oxygen consumption (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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>.
The initial slope of the <inline-formula><mml:math display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>-<inline-formula><mml:math display="inline"><mml:mi>I</mml:mi></mml:math></inline-formula> (Photosynthesis–Irradiance) curve at limiting irradiance <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>
(pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> day<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> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:msup><mml:mo>)</mml:mo><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
the compensation irradiance Ic were calculated according to Eqs. (4) and
(5).

                <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E4"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mtext>Ic</mml:mtext><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mtext>Ek</mml:mtext><mml:mo>×</mml:mo><mml:mtext>Rd</mml:mtext></mml:mrow><mml:mrow><mml:mtext>Pm</mml:mtext><mml:mo>-</mml:mo><mml:mtext>Rd</mml:mtext></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E5"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mtext>Rd</mml:mtext><mml:mtext>Ic</mml:mtext></mml:mfrac></mml:mstyle></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            Oxygen measurements were repeated at 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>
and in the dark at the end of the experiment (7 days of incubation) for all
different light treatments (D, LL, HL) using 10 specimens, to assess their
production or consumption of oxygen at these two light levels (300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>
and in the dark) in all treatments.</p>
      <p>For all conditions (D, LL, HL and Dark-RLC)  Fv/Fm was measured daily at early
afternoon, after a 1-hour dark adaptation period and measurements were
done in triplicate for each Petri dish.</p>
      <p>Rapid light curves were also carried out in all light treatments at the
beginning and end of the experiment, after 1-hour dark adaptation for the
two tested species. Additionally, RLC were carried out daily in an extra
triplicate kept in the dark (Dark-RLC) throughout the duration of the
experiment.</p>
</sec>
<sec id="Ch1.S2.SS8">
  <title>Statistical analysis</title>
      <p>Data are expressed as mean <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> standard deviation (SD) when <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3 or
standard error (SE) when <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 30. Statistical analyses consisted of a
<inline-formula><mml:math display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula> test to compare the foraminifera test mean maximal elongation, a non
parametric test (Kruskal Wallis) to compare the mean chlorophyll
fluorescence of the foraminifera exposed to the different experimental
conditions and a multifactor (experimental conditions (D, LL, HL),
irradiance (0–300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> analysis of variance
(ANOVA) with a Fisher's LSD test to compare the respiration rates at the end
of the experiment. Differences were considered significant at <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.05.
Statistical analyses were carried out using the Statgraphics Centurion
XV.I (StatPoint Technologies, Inc.) software.</p><?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
<sec id="Ch1.S3.SS1">
  <title>Size and biovolume</title>
      <p><italic>Ammonia tepida</italic> specimens were larger than <italic>H. germanica </italic>with a mean
maximal elongation of 390 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 42 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m (SD, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 34) and 366 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 45 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m
(SD, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 122), respectively (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.01, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mrow><mml:mn>121</mml:mn><mml:mo>,</mml:mo><mml:mn>33</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 1.15). This resulted in
cytoplasmic biovolumes equal to 1.20 <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">7</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 3.9 <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> <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:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula>
(SD) and 1.01 <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">7</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 3.65 <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> <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:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> (SD), respectively.</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Chloroplast functionality</title>
      <p>Fresh <italic>Haynesina germanica</italic> and <italic>A. tepida</italic> showed very different spectral reflectance signatures (Fig. 1).
<italic>Haynesina germanica</italic> showed a typical diatom spectral signature with high reflectance in the
infrared region (&gt; 740 nm) and clear absorption features around
585, 630 and 675 nm; the absorption feature around 675 nm corresponds to the
presence of chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>;  the 585 nm feature is the result of fucoxanthin and
the  630 nm absorption feature is the result of chlorophyll <inline-formula><mml:math display="inline"><mml:mi>c</mml:mi></mml:math></inline-formula> (arrows, Fig. 1).
<italic>Ammonia tepida</italic> showed no obvious pigment absorption features apart from 430 nm (Fig. 1).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>Spectral reflectance signatures of <italic>Haynesina germanica</italic>, <italic>Ammonia tepida</italic> and of a benthic diatom in
relative units (<inline-formula><mml:math display="inline"><mml:mi>x</mml:mi></mml:math></inline-formula> axis legend: Wavelength (nm)).</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f01.png"/>

        </fig>

      <p>Epifluorescence images showed a clear effect of the different light
treatments (Dark, Low Light, Hight Light) on <italic>H. germanica</italic> chlorophyll fluorescence
(Fig. 2). Visual observations showed a clear decrease in chlorophyll
fluorescence for the LL and HL treatments from the beginning of the
experiment (Fig. 2a) to the end of a 7-day period of light exposure
(Fig. 2c and d, respectively). Samples kept in the dark did not show an
obvious decrease but showed a more patchy distribution compared to the
beginning of the experiment (Fig. 2b). This was confirmed by a
non-parametric test (Kruskal Wallis) showing that the differences in
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> fluorescence were significant (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.01, Df <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 3,
Fig. 3). It is also noteworthy to mention that there was a large
individual variability within each treatment leading to large standard
errors in spite of the number of replicates (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 30).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>Illustration of <italic>Haynesina germanica</italic> chloroplast content at the beginning <bold>(a)</bold> and at
the end of the experiment for the three experimental conditions, Dark <bold>(b)</bold>,
Low Light <bold>(c)</bold> and High Light <bold>(d)</bold>. Higher colour scale values correspond to
foraminifera emitting more fluorescence and likely containing more
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>; fluorescence in pixel values between 0 and 255, (scale bar <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 50 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m).</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f02.jpg"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>Mean chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> fluorescence (<inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>SE, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 30) at the end
for the three experimental conditions (Dark, Low Light and High Light) and
the beginning (T0) of the experiment using <italic>Haynesina germanica</italic>. Higher mean values likely
corresponded to foraminifera containing more chlorophyll.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f03.png"/>

        </fig>

      <p>Oxygen measurements carried out at the beginning of the experiment (T0)
differed considerably between the two species. <italic>Ammonia tepida</italic> did not show any net oxygen
production although respiration rates measured at 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>
were lower (2485 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 245 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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>
than the ones measured in the dark (3531 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 128 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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>
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>,</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3.7, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 0.02). <italic>Haynesina germanica</italic> showed lower dark
respiration rates (1654 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 785 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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
oxygen production quickly increased with irradiance, showing no
evidence of photoinhibition within the light range used (Fig. 4).
Compensation irradiance (Ic) was reached very quickly, as low as
24 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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> (95 % coefficient bound:
17–30 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>, values calculated from the fitted model Eq. 4) and
the half-saturation constant (Ek) was also reached at very low light levels,
i.e. at 17 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>. No photoinhibition was
observed under the experimental light conditions (0 to 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>, which resulted in an estimation of <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2800 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> 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>
for maximum photosynthetic capacity. The
<inline-formula><mml:math display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>-<inline-formula><mml:math display="inline"><mml:mi>I</mml:mi></mml:math></inline-formula> curve initial slope at limiting irradiance (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> was estimated at
70 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> 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> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (95 %
coefficient bound: 58–88).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Net photosynthesis of <italic>Haynesina germanica</italic> (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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> as a
function of the photon flux density (PFD, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>.
The half-saturation constant, Ek, was found at 17 (13–21), the
dark respiration, Rd, at 1654 (1522–1786) pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> 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>
and the maximum photosynthetic capacity, Pm, at 2845 (2672–3019) pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> 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>.
The Ic, calculated compensation irradiance (24
(17–30) <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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>.
The adjusted <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:mrow></mml:math></inline-formula> of the model was equal to 0.998, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3.</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f04.png"/>

        </fig>

      <p>Oxygen measurements carried out at the end of the experiment (T7) showed
significant different dark and light respiration rates, with light
respiration being lower than dark respiration but not reaching net oxygen
production rates (D, LL, HL) (Table 1). Moreover, respiration rates were
different between conditions (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.001), with significantly lower
respiration rates of specimens incubated under High Light conditions than
those under Dark and Low Light conditions (<inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> &lt; 0.05, Fisher's LSD
test).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1"><caption><p>Light and dark respiration rates (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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> <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> SD
of <italic>Haynesina germanica</italic> in the three experimental conditions (Dark, Low
Light and High Light) at the end of the experiment (Df, degree of freedom,
PFD photon flux density).</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.9}[.9]?><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Condition</oasis:entry>  
         <oasis:entry colname="col2">PFD</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">Respiration rate (pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> d<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></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">D</oasis:entry>  
         <oasis:entry colname="col2">300</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">2452 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 537 </oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">0</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">3542 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 765 </oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">LL</oasis:entry>  
         <oasis:entry colname="col2">300</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">3468 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 305 </oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">0</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">4015 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 110 </oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">HL</oasis:entry>  
         <oasis:entry colname="col2">300</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">1179 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 261 </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">0</oasis:entry>  
         <oasis:entry namest="col3" nameend="col5" align="center">1905 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 235 </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Anova</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">Df</oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mi>F</mml:mi></mml:math></inline-formula> test</oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Condition</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 0.05)</oasis:entry>  
         <oasis:entry colname="col3">2</oasis:entry>  
         <oasis:entry colname="col4">13.1</oasis:entry>  
         <oasis:entry colname="col5">&lt; 0.001</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">PFD</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 0.05)</oasis:entry>  
         <oasis:entry colname="col3">1</oasis:entry>  
         <oasis:entry colname="col4">5.4</oasis:entry>  
         <oasis:entry colname="col5">0.026</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Interaction</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 0.05)</oasis:entry>  
         <oasis:entry colname="col3">2</oasis:entry>  
         <oasis:entry colname="col4">0.3</oasis:entry>  
         <oasis:entry colname="col5">0.78</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <p>PAM fluorescence rapid light curve (RLC) parameters (<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, rETRmax, Ek
and Eopt) showed significant differences between foraminiferal species and
over the duration of the experiment (Figs. 5 and 6). Highest rETRmax,
<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and Eopt were always observed in <italic>H. germanica</italic>. After only one starvation day <italic>A. tepida</italic>
RLC parameters dropped to zero or close to zero. In contrast, <italic>H. germanica</italic> RLC
parameters showed a slow decrease throughout the experiment (Figs. 5 and
6)  with rETRmax and <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> decreasing from 6 to 4 and 0.22 to 0.15,
respectively (Figs. 6a and b). The parameters Ek and Eopt stayed constant
over the 7 days of the experiment, with values oscillating around 30 and 90,
respectively (Fig. 6c and d).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5"><caption><p>Rapid light curves (RLC, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3) expressed as the relative
electron transport rate (rETR) as a function of the photosynthetic active
radiation (PAR in <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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 <italic>Haynesina germanica</italic> (black lines) and
<italic>Ammonia tepida</italic> (black dashed lines) during the 7 days of the experiment.</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f05.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p>Rapid light curve (RLC, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3) parameters for <italic>Haynesina germanica</italic> (Dark-RLC) and
<italic>Ammonia tepida</italic> maintained in the dark during the experiment, Alpha is the initial slope of
the RLC at limiting irradiance, rETRmax is the maximum relative electron
transport rate, Ek is the light saturation coefficient and Eopt is the
optimum light, all of them were estimated by adjusting the experimental data
to fit the model of Platt et al. (1980).</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f06.png"/>

        </fig>

      <p>PSII maximum quantum yields (Fv/Fm) were clearly affected by light and
time (Fig. 7). Both species showed high initial  Fv/Fm values, i.e. &gt; 0.6
and 0.4 for <italic>H. germanica</italic> and <italic>A. tepida</italic>, respectively  (Fig. 7).
However, while <italic>A. tepida</italic> Fv/Fm values quickly
decreased to zero after only one starvation day, <italic>H. germanica</italic> exhibited a large
variability between light conditions (D, LL, HL) throughout the duration of
the experiment (Fig. 7); decreasing from 0.65 to 0.55 in darkness (D),
from 0.65 to 0.35 under low light (LL) conditions and from 0.65 to 0.20
under high light (HL). Using these  Fv/Fm decreases, <italic>H. germanica </italic>kleptoplast functional times
were estimated between 11 and 21 days in the dark (D), 9–12 days in low light
(LL) and 7–8 days in high light (HL), depending on whether or not an exponential or linear
model was applied. <italic>Ammonia tepida</italic> chloroplast functional times were estimated between 1 and 2 days (exponential and linear model, respectively) and light exposure reduced
the functional time to less than 1 day (data not shown).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><caption><p>Maximum quantum efficiency of the photosystem II (Fv/Fm, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 3)
during the experiment for the different applied conditions (Dark, Low Light
and High Light) and species (<italic>Haynesina germanica</italic> and <italic>Ammonia tepida</italic>).</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2715/2016/bg-13-2715-2016-f07.png"/>

        </fig>

<?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <title>Chloroplast functionality</title>
      <p>Our results clearly show that only <italic>H. germanica</italic> was capable of carrying out net
photosynthesis. <italic>Haynesina germanica</italic> had typical diatom reflectance spectra (Fig. 1), showing
the three major diatom pigment absorption features: chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>,
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>c</mml:mi></mml:math></inline-formula>, and fucoxanthin (Meleder et al., 2003, 2013; Jesus et al., 2008;
Kazemipour et al., 2012). Conversely, in <italic>A. tepida</italic> these
absorption features were not detected, suggesting that diatom pigments
ingested by this species were quickly digested and degraded to a degree
where they were no longer detected by spectral reflectance measurements.
These non-destructive reflectance measurements are thus in accordance with
other studies on benthic foraminifera pigments by HPLC showing that <italic>H. germanica</italic> feed on
benthic diatoms (Knight and Mantoura, 1985). Similarly, Knight and Mantoura (1985) also detected higher concentrations and less degraded diatom pigments
in <italic>H. germanica</italic> than in <italic>A. tepida.</italic></p>
      <p>Furthermore, <italic>H. germanica</italic> has the ability to produce oxygen from low to relatively high
irradiance, as shown by the low compensation point (Ic) of 24 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>
and the high onset of light saturation
(&gt; 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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> (Fig. 4). Thus, <italic>H. germanica</italic>
seems to be well adapted to cope with the high light variability observed in
intertidal sediments that can range from very high irradiance levels
(&gt; 1000 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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 the surface of
the sediment during low tide to very low levels within the sediment matrix
or during high tide in turbid mudflat waters. <italic>Ammonia tepida</italic> was found to carry out aerobic
respiration, but respiration rates measured at 300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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> were lower than those measured in the dark. We thus
suppose that in <italic>A. tepida</italic> oxygen production by ingested diatom or chloroplasts might
be possible, provided that this species is constantly supplied with fresh
diatoms. However, another possibility to explain this reduction in oxygen
consumption could be a decrease of its metabolism or activity under light
exposure. The light and dark oxygen production or consumption values
measured for both species are in accordance with previous studies (Geslin et
al., 2011).</p>
      <p>According to Lopez (1979), measured oxygen data can be used to estimate <italic>H. germanica</italic>
carbon fixation rates. Thus, using 1000 pmol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> cell<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> 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> at
300 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>, <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 200 to 4000 cells
per 50 cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> in the top 0.5 cm (Morvan et al., 2006; Bouchet et al., 2007)
and assuming that photosynthesis produced one mol O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> per mol of C
fixed, <italic>H. germanica</italic> primary production would be between 1.8 <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">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
4.0 <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">4</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> mol 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>. This is a very low value
compared to microphytobenthos primary production in Atlantic mudflat
ecosystems, which usually range from 1.5 to 5.9 mol 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>
(e.g. Brotas and Catarino, 1995, reviewed in MacIntyre et al., 1996). The
estimated values represent thus less than 0.1 % of microphytobenthos
fixated carbon and are in the same range of values than what has been
described by Lopez (1979) using <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>14</mml:mn></mml:msup></mml:math></inline-formula>C radioactive tracers. These results
should be interpreted with caution because a wide variety of factors
probably affect <italic>H. germanica</italic> in situ primary production, e.g. diatom availability, kleptoplast
densities, nutrient supply, light exposure, sea water turbidity, local
biogeochemical processes and migration capability are all factors that can
potentially affect <italic>H. germanica</italic> kleptoplast functionality. Nevertheless, although carbon
fixation seems not to be relevant at a global scale, the oxygen production
could be important at a microscale and relevant in local mineralization
processes in/on mudflat sediments (e.g. iron, ammonium, manganese).</p>
      <p>At sampling time (T0) <italic>H. germanica</italic> rETR and  Fv/Fm values were similar to microphytobenthic
species (i.e.  Fv/Fm &gt; 0.65) (Perkins et al., 2001), suggesting that the
kleptoplast PSII and electron transport chain were not much affected after
incorporation in the foraminifers' cytoplasm. In contrast, <italic>A. tepida</italic> Fv/Fm and RLC
parameters were already much lower on the sampling day and quickly decreased
to almost zero within 24 h, suggesting that plastids were not stable
inside the <italic>A. tepida</italic> cytoplasm. Complete diatoms inside <italic>A. tepida</italic> were already observed in
feeding studies (Le Kieffre, pers. com), this low  Fv/Fm value might thus come
from recently ingested diatoms by <italic>A. tepida</italic>.  Fv/Fm has previously been used to determine
kleptoplast functional times and to follow decrease in kleptoplast
efficiency in other kleptoplastic organisms, e.g. the sea slug <italic>Elysia virid</italic>is (Vieira et
al., 2009).  Fv/Fm measurements carried out on <italic>H. germanica</italic> at different light conditions
showed that light had a significant effect on the estimation of kleptoplast
functional time, with the longest functional time estimated at 21 days for
dark conditions. This time frame would qualify <italic>H. germanica</italic> as a long-term kleptoplast
retention species (Clark et al., 1990); however, our 7 days estimation
for the high light treatment would place <italic>H. germanica</italic> in the medium-term retention
group. This clearly shows that light exposure has an important effect on
this species kleptoplast functionality. Concerning <italic>A. tepida, </italic>the short dark diatom or
chloroplast functional time (&lt; 2 days) places this species directly
in the short or medium-term retention group.</p>
      <p>Additionally, <italic>H. germanica</italic> kept in darkness showed a slow decrease of the RLC
parameters, <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and rETRmax, throughout the 7 experimental days;
this decrease is likely related to overall degradation of the
light-harvesting complexes and of other components of the photosynthetic
apparatus, which gradually induced a reduction of light harvesting
efficiency and of carbon metabolism. This decrease was amplified in low
and high irradiance and it should be pointed out that the actual light level
of the HL treatment (i.e. 70 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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: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> is very
low compared to irradiances in their natural environment, which are
easily going above 1000 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol photons 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>, showing that
the foraminifera kleptoplasts lack the high photoregulation capacity
exhibited by the benthic diatoms that they feed upon (Cartaxana et al.,
2013). This is consistent with the observation at the end of the experiment
that no net oxygen production was occurring under the different light
conditions. Nevertheless, a small difference was still found between dark
and light respiration (Table 1), suggesting that some oxygen production was
still occurring but it was not sufficient to compensate for the respiration
oxygen consumption. We also noticed that the respiration was higher in the
foraminifera maintained in low light and dark conditions in comparison to
the high light foraminifera. In the line of the lower  Fv/Fm values observed, this
suggests that kleptoplasts and possibly other metabolic pathways might have
been damaged by the excess light. Clearly, in <italic>H. germanica</italic> light exposure had a
strong effect on PSII maximum quantum efficiency and on the retention of
functional kleptoplasts (Fig.  7), which can explain the absence of net
oxygen production after the 7 days of the experiments. Comparable results
for <italic>H. germanica</italic> were also obtained by counting the number of chloroplasts over time
with cells exposed or not to light (Lopez, 1979). One of the most probable
explanations for the observed  Fv/Fm decrease is the gradual inactivation of the
protein D1 in PSII reaction centres. This protein is an essential component
in the electron transport chain and its turnover rate is frequently the
limiting factor in PSII repair rates (reviewed in Campbell and
Tyystjärvi, 2012). Normally, protein D1 is encoded in the chloroplast and
is rapidly degraded and resynthesized under light exposure with a turnover
correlated to irradiance (Tyystjärvi and Aro, 1996). However, although D1
is encoded by the chloroplast genome, its synthesis and concomitant PSII
recovery require further proteins that are encoded by the algal nuclear
genome (Yamaguchi et al., 2005). Thus, when D1 turnover is impaired it will
induce an  Fv/Fm decrease correlated to irradiance (Tyystjärvi and Aro, 1996)
consistent to what was observed in the present study. In another deep sea
benthic species   (<italic>Nonionella stella</italic>) the D1 and other plastid proteins (RuBisCO and FCP
complex) were still present in the foraminifer 1 year after sampling
(Grzymski et al., 2002). This shows that some foraminifera can retain both
nuclear (FCP) and chloroplast (D1 and RuBisCO) encoded proteins. However,
contrary to <italic>H. germanica</italic>, <italic>N. stella</italic> lives in deeper environments never exposed to light and thus
is unlikely to carry out oxygenic photosynthesis (Grzymski et al., 2002).
This fundamental difference could explain why kleptoplast functional times
are much longer in <italic>N. stella</italic>, reaching up to 1 year in specimens kept in darkness
(Grzymski et al., 2002). On the other hand, it has been shown that isolated
chloroplasts are able to function for several months in Sacoglossan sea
slugs provided with air and light in aquaria (Green et al., 2001; Rumpho et
al., 2001), which demonstrates the existence of interactions between the
kleptoplast and the host genomes, and/or of mechanisms facilitating and
supporting such long-lasting associations.   In <italic>H. germanica</italic> exposed to high light it is
also possible that reactive oxygen species (ROS) production rates of the
sequestered chloroplasts might exceed the foraminifera capacity to eliminate
those ROS, thus inducing permanent damage to the foraminifera. This ROS
production could also eventually damage the kleptoplasts resulting in higher
kleptoplast degradation rates.</p>
</sec>
<sec id="Ch1.S4.SS2">
  <title>Possible advantages of kleptoplasty for intertidal benthic
foraminifera</title>
      <p>Much is still unknown about the relationship between kleptoplastic benthic
foraminifera and their sequestered chloroplasts. The relevance of the
photosynthetic metabolism compared to predation or organic matter
assimilation is unknown; however, it would be of great interest to
understand the kleptoplast role in the foraminiferal total energy budget.
Oxygenic photosynthesis comprises multiple reactions leading to the
transformation of inorganic carbon to carbohydrates. However, to produce
these carbohydrates all the light-driven reactions have to be carried out,
as well as the Calvin cycle reactions. With fresh kleptoplasts this
hypothesis seems possible (e.g. Lopez, 1979), especially if the plastid
proteins are still present and functional. However, we showed that the
maximum quantum efficiency of the PSII decreased quickly under light
exposure, suggesting that substantial direct carbohydrate production is
unlikely without constant chloroplast replacement. Conversely, the
production of intermediate photosynthetate products such as adenosine
triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH)
could be possible and would be of metabolic value for the foraminifera. It
is also possible that  in situ the foraminifera have better photoregulation
capacities. Not only will they have easy access to fresh diatom
chloroplasts, as <italic>H. germanica</italic> is mainly living in the first few millimetres of the superficial
sediment (Alve and Murray, 2001; Thibault de Chanvalon et al., 2015), but they
will also have the possibility of migrating within the sediment (Gross, 2000)
using this behavioural feature to enhance their photoregulation capacity,
similar to what is observed in benthic diatoms from microphytobenthic
biofilms (e.g. Jesus et al., 2006; Mouget et al., 2008; Perkins et al., 2010).
However, below the photic limit (max 2 to 3 mm in estuarine sediments
reviewed in MacIntyre et al., 1996; Cartaxana et al., 2011) it is unlikely
that oxygenic photosynthesis will occur, even if live <italic>H. germanica</italic> are also found below
this limit (Thibault de Chanvalon et al., 2015; Cesbron et al., 2016).</p>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusion</title>
      <p>Comparing <italic>H. germanica</italic> with <italic>A. tepida</italic> showed that the former species potentially has the capacity
of retaining functional kleptoplasts up to 21 days, much longer than <italic>A. tepida</italic> that
showed almost no PSII activity after 24 h. Nevertheless, the capacity of
<italic>H. germanica</italic> to keep functional kleptoplasts was significantly decreased by exposing it
even to low irradiance levels, which resulted in low  Fv/Fm values and decreased
oxygen production. This shows clearly that in our experimental conditions,
<italic>H. germanica</italic> had reduced photoregulation capacities. These results emphasize that
studies on kleptoplast photophysiology of benthic foraminifera must be
interpreted with care, as results are strongly influenced by the
foraminiferal light history before incubation. Additionally, this study
shows that the cellular machinery necessary for chloroplast maintenance is
unlikely to be completely functional, suggesting that <italic>H. germanica</italic> has to continuously
renew its chloroplasts to keep them functional. We hypothesize that
kleptoplasts might have an added value by providing extra carbon, mainly
under light exposure, but also as energy stock to be digested during food
impoverished periods, in dark or light conditions.</p>
</sec>

      
      </body>
    <back><ack><title>Acknowledgements</title><p>This study is part of the EC2CO project “ForChlo” supported by the CNRS.
This study is strongly supported by the Region Pays de la Loire (Post-doc
position of the first author and “COSELMAR” and “Fresco” projects).<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>
Edited by:  J. Middelburg</p></ack><ref-list>
    <title>References</title>

      <ref id="bib1.bib1"><label>1</label><mixed-citation>
Alve, E. and Murray, J. W.: Temporal variability in vertical distributions of
live (stained) intertidal foraminifera, southern England, J. Foramin.
Res., 31, 12–24, 2001.</mixed-citation></ref>
      <ref id="bib1.bib2"><label>2</label><mixed-citation>Austin, H. A., Austin, W. E., and Paterson, D. M.: Extracellular cracking and
content removal of the benthic diatom <italic>Pleurosigma angulatum</italic> (Quekett) by the benthic foraminifera
<italic>Haynesina germanica</italic> (Ehrenberg), Mar. Micropaleontol., 57, 68–73, 2005.</mixed-citation></ref>
      <ref id="bib1.bib3"><label>3</label><mixed-citation>
Bernhard, J. M. and Bowser, S. S.: Benthic foraminifera of dysoxic sediments:
chloroplast sequestration and functional morphology, Earth-Sci. Rev., 46,
149–165, 1999.</mixed-citation></ref>
      <ref id="bib1.bib4"><label>4</label><mixed-citation>
Bouchet, V. M. P., Debenay, J.-P., Sauriau, P.-G., Radford-Knoery, J., and
Soletchnik, P.: Effects of short-term environmental disturbances on living
benthic foraminifera during the Pacific oyster summer mortality in the
Marennes-Oleron Bay (France), Mar. Environ. Res., 64, 358–383, 2007.</mixed-citation></ref>
      <ref id="bib1.bib5"><label>5</label><mixed-citation>
Bouchet, V. M. P., Sauriau, P.-G., Debenay, J.-P., Mermillod-Blondin, F.,
Schmidt, S., Amiard, J.-C., and Dupas, B.: Influence of the mode of
macrofauna-mediated bioturbation on the vertical distribution of living
benthic foraminifera: First insight from axial tomodensitometry, J. Exp.
Mar. Biol. Ecol., 371, 20–33, 2009.</mixed-citation></ref>
      <ref id="bib1.bib6"><label>6</label><mixed-citation>
Brotas, V. and Catarino, F.: Microphytobenthos primary production of Tagus
estuary intertidal flats (Portugal), Neth. J. Aquat. Ecol., 29, 333–339,
1995.</mixed-citation></ref>
      <ref id="bib1.bib7"><label>7</label><mixed-citation>
Cartaxana, P., Ruivo, M., Hubas, C., Davidson, I., Serôdio, J., and
Jesus, B.: Physiological versus behavioral photoprotection in intertidal
epipelic and epipsammic benthic diatom communities, J. Exp. Mar. Biol. Ecol.,
405, 120–127, 2011.</mixed-citation></ref>
      <ref id="bib1.bib8"><label>8</label><mixed-citation>
Cartaxana, P., Domingues, N., Cruz, S., Jesus, B., Laviale, M., Serôdio,
J., and Marques da Silva, J.: Photoinhibition in benthic diatom assemblages
under light stress, Aquat. Microb. Ecol., 70, 87–92, 2013.</mixed-citation></ref>
      <ref id="bib1.bib9"><label>9</label><mixed-citation>
Campbell, D. A.  and Tyystjarvi, E.: Parameterization of photosystem II
photoinactivation and repair, BBA-Bioenergetics, 1817,
258–265, 2012.</mixed-citation></ref>
      <ref id="bib1.bib10"><label>10</label><mixed-citation>Cesbron, F., Geslin, E., Jorissen, F. J., Delgard, M. L., Charrieau, L.,
Deflandre, B., Jézéquel, D., Anschutz, P., and Metzger, E.: Vertical distribution
and respiration rates of benthic foraminifera: Contribution to aerobic
remineralization in intertidal mudflats covered by <italic>Zostera noltei</italic> meadows, Estuar. Coast.
Shelf S., in press, 2016.</mixed-citation></ref>
      <ref id="bib1.bib11"><label>11</label><mixed-citation>Clark, K. B., Jensen, K. R., and Stirts, H. M.: Survey for functional
kleptoplasty among West Atlantic Ascoglossa (<inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula>Sacoglossa) (Mollusca:
Opisthobranchia), Veliger, 33, 339–345, 1990.</mixed-citation></ref>
      <ref id="bib1.bib12"><label>12</label><mixed-citation>Correia, M. J. and Lee, J. J.: Chloroplast retention by <italic>Elphidium excavatum</italic> (Terquem). Is it a
selective process?, Symbiosis, 29, 343–355, 2000.</mixed-citation></ref>
      <ref id="bib1.bib13"><label>13</label><mixed-citation>Correia, M. J. and Lee, J. J.: Fine structure of the plastids retained by the
foraminifer <italic>Elphidium excavatum</italic> (Terquem), Symbiosis, 32,  15–26, 2002a.</mixed-citation></ref>
      <ref id="bib1.bib14"><label>14</label><mixed-citation>Correia, M. J. and Lee, J. J.: How long do the plastids retained by <italic>Elphidium excavatum</italic> (Terquem)
last in their host?, Symbiosis, 32, 27–37, 2002b.</mixed-citation></ref>
      <ref id="bib1.bib15"><label>15</label><mixed-citation>Costa, J., Gimenez-Casalduero, F., Melo, R., and  Jesus, B.: Colour morphotypes
of <italic>Elysia timida</italic> (Sacoglossa, Gastropoda) are determined by light acclimation in food
algae, Aquat. Biol., 17, 81–89, 2012.</mixed-citation></ref>
      <ref id="bib1.bib16"><label>16</label><mixed-citation>
Curtis, N. E., Middlebrooks, M. L., Schwartz, J. A., and Pierce, S. K.: PAM
analysis of 3 sacoglossan species reveals differences in photosynthetic
function and chloroplast longevity, Integr. Comp. Biol., 53, 272–272, 2013.</mixed-citation></ref>
      <ref id="bib1.bib17"><label>17</label><mixed-citation>
Debenay, J.-P., Guillou, J.-J., Redois, F., and Geslin, E.: Distribution
trends of foraminiferal assemblages in paralic environments, in:
Environmental Micropaleontology, edited by: Martin, R. E., Springer
US, New York, 39–67, 2000.</mixed-citation></ref>
      <ref id="bib1.bib18"><label>18</label><mixed-citation>
Debenay, J. P., Bicchi, E., Goubert, E., and du Chatelet, E. A.:
Spatio-temporal distribution of benthic foraminifera in relation to estuarine
dynamics (Vie estuary, Vendee, W France), Estuar. Coast. Shelf S., 67,
181–197, 2006.</mixed-citation></ref>
      <ref id="bib1.bib19"><label>19</label><mixed-citation>
Eberhard, S., Finazzi, G., and Wollman, F.-A.: The dynamics of
photosynthesis, Annu. Rev. Genet., 42,   463–515, 2008.</mixed-citation></ref>
      <ref id="bib1.bib20"><label>20</label><mixed-citation>
Evertsen, J., Burghardt, I., Johnsen, G., and Wagele, H.: Retention of
functional chloroplasts in some sacoglossans from the Indo-Pacific and
Mediterranean, Mar. Biol., 151, 2159–2166, 2007.</mixed-citation></ref>
      <ref id="bib1.bib21"><label>21</label><mixed-citation>
Falkowski, P. G. and Raven, J. A.: Aquatic photosynthesis, second Edn.,
Princeton Universty Press, Princeton, 2007.</mixed-citation></ref>
      <ref id="bib1.bib22"><label>22</label><mixed-citation>
Geslin, E., Risgaard-Petersen, N., Lombard, F., Metzger, E., Langlet, D., and
Jorissen, F.: Oxygen respiration rates of benthic foraminifera as measured
with oxygen microsensors, J. Exp. Mar. Biol. Ecol., 396, 108–114, 2011.</mixed-citation></ref>
      <ref id="bib1.bib23"><label>23</label><mixed-citation>Goldstein, S. T., Habura, A., Richardson, E. A., and Bowser, S. S.:
<italic>Xiphophaga minuta</italic>, and <italic>X. allominuta</italic>, nov. gen., nov. spp.,
new monothalamid Foraminifera from coastal Georgia (USA): cryptic species,
gametogenesis, and an unusual form of chloroplast sequestration, J. Foramin.
Res., 40, 3–15, 2010.</mixed-citation></ref>
      <ref id="bib1.bib24"><label>24</label><mixed-citation>Goldstein, S. T., Bernhard, J. M., and Richardson, E. A. Chloroplast
sequestration in the foraminifer <italic>Haynesina germanica</italic>: Application of
high pressure freezing and freeze substitution, Microsc. Microanal., 10,
1458–1459, 2004.</mixed-citation></ref>
      <ref id="bib1.bib25"><label>25</label><mixed-citation>
Gooday, A. J.: Meiofaunal foraminiferans from the bathyal Porcupine Seabight
(northeast Atlantic): size structure, standing stock, taxonomy composition,
species diversity and vertical distribution in the sediment, Deep-Sea Res.
Pt. I, 33, 1345–1373, 1986.</mixed-citation></ref>
      <ref id="bib1.bib26"><label>26</label><mixed-citation>
Green, B. J., Li, W.-Y., Manhart, J. R., Fox, T. C., Summer, E. J., Kennedy, R. A.,
Pierce, S. K., and Rumpho, M. E.: Mollusc-algal chloroplast endosymbiosis.
Photosynthesis, thylakoid protein maintenance, and chloroplast gene
expression continue for many months in the absence of the algal nucleus,
Plant Physiol., 124, 331–342, 2001.</mixed-citation></ref>
      <ref id="bib1.bib27"><label>27</label><mixed-citation>
Gross, O.: Influence of temperature, oxygen and food availability on the
migrational activity of bathyal benthic foraminifera: evidence by microcosm
experiments, Hydrobiologia, 426, 123–137, 2000.</mixed-citation></ref>
      <ref id="bib1.bib28"><label>28</label><mixed-citation>Grzymski, J., Schofield, O. M., Falkowski, P. G., and Bernhard, J. M.: The
function of plastids in the deep-sea benthic foraminifer, <italic>Nonionella stella</italic>, Limnol.
Oceanogr., 47, 1569–1580, 2002.</mixed-citation></ref>
      <ref id="bib1.bib29"><label>29</label><mixed-citation>
Hannah, F., Rogerson, A., and Laybournparry, J.: Respiration rates and
biovolumes of common benthic foraminifera (Protozoa), J. Mar. Biol. Assoc.
UK, 74, 301–312, 1994.</mixed-citation></ref>
      <ref id="bib1.bib30"><label>30</label><mixed-citation>
Hayward, B. W., Holzmann, M., Grenfell, H. R., Pawlowski, J., and Triggs, C. M.:
Morphological distinction of molecular types in Ammonia – towards a
taxonomic revision of the world's most commonly misidentified foraminifera,
Mar. Micropaleontol., 50, 237–271, 2004.</mixed-citation></ref>
      <ref id="bib1.bib31"><label>31</label><mixed-citation>
Høgslund, S., Revsbech, N. P., Cedhagen, T., Nielsen, L. P., and Gallardo,
V. A.: Denitrification, nitrate turnover, and aerobic respiration by benthic
foraminiferans in the oxygen minimum zone off Chile, J. Exp. Mar. Biol.
Ecol., 359, 85–91, 2008.</mixed-citation></ref>
      <ref id="bib1.bib32"><label>32</label><mixed-citation>
Jesus, B., Perkins, R. G., Consalvey, M., Brotas, V., and Paterson, D. M.:
Effects of vertical migrations by benthic microalgae on fluorescence
measurements of photophysiology, Mar. Ecol.-Prog. Ser., 315, 55–66, 2006.</mixed-citation></ref>
      <ref id="bib1.bib33"><label>33</label><mixed-citation>
Jesus, B., Mouget, J.-L., and Perkins, R. G.: Detection of diatom xanthophyll
cycle using spectral reflectance, J. Phycol., 44, 1349–1359, 2008.</mixed-citation></ref>
      <ref id="bib1.bib34"><label>34</label><mixed-citation>
Jesus, B., Brotas, V., Ribeiro, L., Mendes, C. R., Cartaxana, P., and
Paterson, D. M.: Adaptations of microphytobenthos assemblages to sediment
type and tidal position, Cont. Shelf Res., 29, 1624–1634, 2009.</mixed-citation></ref>
      <ref id="bib1.bib35"><label>35</label><mixed-citation>Jesus, B., Ventura, P., and Calado, G.: Behaviour and a functional
xanthophyll cycle enhance photo-regulation mechanisms in the solar-powered
sea slug <italic>Elysia timida</italic> (Risso, 1818), J. Exp. Mar. Biol. Ecol., 395, 98–105,
2010.</mixed-citation></ref>
      <ref id="bib1.bib36"><label>36</label><mixed-citation>
Kazemipour, F., Launeau, P., and Méléder, V.: Microphytobenthos
biomass mapping using the optical model of diatom biofilms: Application to
hyperspectral images of Bourgneuf Bay, Remote Sens. Environ., 127, 1–13,
2012.</mixed-citation></ref>
      <ref id="bib1.bib37"><label>37</label><mixed-citation>
Knight, R. and Mantoura, R. F. C.: Chlorophyll and carotenoid pigments in
foraminifera and their symbiotic algae: analysis by high performance liquid
chromatography, Mar. Ecol.-Prog. Ser., 23, 241–249, 1985.</mixed-citation></ref>
      <ref id="bib1.bib38"><label>38</label><mixed-citation>Lee, J. J., Lanners, E., and Ter Kuile, B.: The retention of chloroplasts by
the foraminifera <italic>Elphidium crispum</italic>, Symbiosis, 5, 45–60, 1988.</mixed-citation></ref>
      <ref id="bib1.bib39"><label>39</label><mixed-citation>
Li, Y. H. and Gregory, S.: Diffusion of ions in sea-water and deep-sea
sediments, Geochim. Cosmochim. Ac., 38, 703–714, 1974.</mixed-citation></ref>
      <ref id="bib1.bib40"><label>40</label><mixed-citation>
Lopez, E.: Algal chloroplasts in the protoplasm of three species of benthic
foraminifera: taxonomic affinity, viability and persistence, Mar. Biol., 53,
201–211, 1979.</mixed-citation></ref>
      <ref id="bib1.bib41"><label>41</label><mixed-citation>
MacIntyre, H. L., Geider, R. J., and Miller, D. C.: Microphytobenthos: The
ecological role of the “secret garden” of unvegetated, shallow-water
marine habitats .1. Distribution, abundance and primary production,
Estuaries, 19, 186–201, 1996.</mixed-citation></ref>
      <ref id="bib1.bib42"><label>42</label><mixed-citation>Marchetti, J., Bougaran, G., Jauffrais, T., Lefebvre, S., Rouxel, C.,
Saint-Jean, B., Lukomska, E., Robert, R., and Cadoret, J. P.: Effects of blue
light on the biochemical composition and photosynthetic activity of
<italic>Isochrysis</italic> sp. (T-iso), J. Appl. Phycol., 25, 109–119, 2013.</mixed-citation></ref>
      <ref id="bib1.bib43"><label>43</label><mixed-citation>
Meleder, V., Barille, L., Launeau, P., Carrere, V., and Rince, Y.:
Spectrometric constraint in analysis of benthic diatom biomass using
monospecific cultures, Remote Sens. Environ., 88, 386–400, 2003.</mixed-citation></ref>
      <ref id="bib1.bib44"><label>44</label><mixed-citation>
Meleder, V., Laviale, M., Jesus, B., Mouget, J. L., Lavaud, J., Kazemipour,
F., Launeau, P., and Barille, L.: In vivo estimation of pigment composition
and optical absorption cross-section by spectroradiometry in four aquatic
photosynthetic micro-organisms, J. Photoch. Photobio. B, 129,
115–124, 2013.</mixed-citation></ref>
      <ref id="bib1.bib45"><label>45</label><mixed-citation>
Moodley, L., Middelburg, J. J., Boschker, H. T. S., Duineveld, G. C. A., Pel, R.,
Herman, P. M. J., and Heip, C. H. R.: Bacteria and Foraminifera: key players in a
short-term deep-sea benthic response to phytodetritus, Mar. Ecol.-Prog. Ser.,
236:, 23–29, 2002.</mixed-citation></ref>
      <ref id="bib1.bib46"><label>46</label><mixed-citation>
Morvan, J., Debenay, J.-P., Jorissen, F., Redois, F., Beneteau, E.,
Delplancke, M., and Amato, A.-S. Patchiness and life cycle of intertidal
foraminifera: Implication for environmental and paleoenvironmental
interpretation, Mar. Micropaleontol., 61, 131–154, 2006.</mixed-citation></ref>
      <ref id="bib1.bib47"><label>47</label><mixed-citation>
Mouget, J.-L., Perkins, R. G., Consalvey, M., and Lefebvre, S.: Migration or
photoacclimation to prevent photoinhibition and UV-B damage in marine
microphytobenthic communities, Aquat. Microb. Ecol., 52, 223–232, 2008.</mixed-citation></ref>
      <ref id="bib1.bib48"><label>48</label><mixed-citation>
Papacek, S., Celikovsky, S., Rehak, B., and Stys, D.: Experimental design for
parameter estimation of two time-scale model of photosynthesis and
photoinhibition in microalgae, Math. Comput. Simulat., 80, 1302–1309, 2010.</mixed-citation></ref>
      <ref id="bib1.bib49"><label>49</label><mixed-citation>
Pascal, P.-Y., Dupuy, C., Richard, P., Mallet, C., du Chatelet, E. A., and
Niquil, N.: Seasonal variation in consumption of benthic bacteria by meio-
and macrofauna in an intertidal mudflat, Limnol. Oceanogr., 54, 1048–1059,
2009.</mixed-citation></ref>
      <ref id="bib1.bib50"><label>50</label><mixed-citation>
Perkins, R. G., Underwood, G. J. C., Brotas, V., Snow, G. C., Jesus, B., and
Ribeiro, L.: Responses of microphytobenthos to light: primary production and
carbohydrate allocation over an emersion period, Mar. Ecol.-Prog. Ser., 223,
101–112, 2001.</mixed-citation></ref>
      <ref id="bib1.bib51"><label>51</label><mixed-citation>
Perkins, R. G., Mouget, J.-L., Lefebvre, S., and Lavaud, J.: Light response
curve methodology and possible implications in the application of chlorophyll
fluorescence to benthic diatoms, Mar. Biol., 149, 703–712, 2006.</mixed-citation></ref>
      <ref id="bib1.bib52"><label>52</label><mixed-citation>
Perkins, R. G., Lavaud, J., Serodio, J., Mouget, J. L., Cartaxana, P., Rosa,
P., Barille, L., Brotas, V., and Jesus, B. M.: Vertical cell movement is a
primary response of intertidal benthic biofilms to increasing light dose,
Mar. Ecol.-Prog. Ser., 416, 93–103, 2010.</mixed-citation></ref>
      <ref id="bib1.bib53"><label>53</label><mixed-citation>Pillet, L. and Pawlowski, J.: Transcriptome analysis of foraminiferan
<italic>Elphidium margaritaceum</italic> questions the role of gene transfer in
kleptoplastidy, Mol. Biol. Evol., 30, 66–69, 2013.</mixed-citation></ref>
      <ref id="bib1.bib54"><label>54</label><mixed-citation>
Pillet, L., de Vargas, C., and Pawlowski, J.: Molecular identification of
sequestered diatom chloroplasts and kleptoplastidy in foraminifera, Protist,
162, 394–404, 2011.</mixed-citation></ref>
      <ref id="bib1.bib55"><label>55</label><mixed-citation>
Pina-Ochoa, E., Hogslund, S., Geslin, E., Cedhagen, T., Revsbech, N. P., Nielsen, L. P., Schweizer, M., Jorissen, F., Rysgaard, S., and Risgaard-Petersen, N.: Widespread occurrence
of nitrate storage and denitrification among foraminifera and gromiida,
P. Natl. Acad. Sci. USA, 107, 1148–1153, 2010.</mixed-citation></ref>
      <ref id="bib1.bib56"><label>56</label><mixed-citation>
Platt, T., Gallegos, C. L., and Harrison, W. G.: Photoinhibition of
photosynthesis in natural assemblages of marine phytoplankton, J. Mar. Res.,
38, 687–701, 1980.</mixed-citation></ref>
      <ref id="bib1.bib57"><label>57</label><mixed-citation>
Revsbech, N. P.: An oxygen microsensor with a guard cathode, Limnol.
Oceanogr., 34, 474–478, 1989.</mixed-citation></ref>
      <ref id="bib1.bib58"><label>58</label><mixed-citation>Rink, S., Kuhl, M., Bijma, J., and Spero, H. J.: Microsensor studies of
photosynthesis and respiration in the symbiotic foraminifer <italic>Orbulina universa</italic>, Mar.
Biol., 131, 583–595, 1998.</mixed-citation></ref>
      <ref id="bib1.bib59"><label>59</label><mixed-citation>
Risgaard-Petersen, N., Langezaal, A. M., Ingvardsen, S., Schmid, M. C.,
Jetten, M. S. M., Op den Camp, H. J. M., Derksen, J. W. M., Pina-Ochoa, E.,
Eriksson, S. P., Nielsen, L. P., Revsbech, N. P., Cedhagen, T., and van der
Zwaan, G. J.: Evidence for complete denitrification in a benthic foraminifer,
Nature, 443, 93–96, 2006.</mixed-citation></ref>
      <ref id="bib1.bib60"><label>60</label><mixed-citation>Rumpho, M. E., Summer, E. J., Green, B. J., Fox, T. C., and Manhart, J. R.:
Mollusc/algal chloroplast symbiosis: how can isolated chloroplasts continue
to function for months in the cytosol of a sea slug in the absence of an
algal nucleus?, Zoology, 104, 303–312, 2001.
 </mixed-citation></ref><?xmltex \hack{\newpage}?>
      <ref id="bib1.bib61"><label>61</label><mixed-citation>Serodio, J., Pereira, S., Furtado, J., Silva, R., Coelho, H., and Calado, R.:
In vivo quantification of kleptoplastic chlorophyll a content in the
“solar-powered” sea slug <italic>Elysia viridis</italic> using optical methods:
spectral reflectance analysis and PAM fluorometry, Photochem. Photobio. S.,
9, 68–77, 2010.</mixed-citation></ref>
      <ref id="bib1.bib62"><label>62</label><mixed-citation>Thibault de Chanvalon, A., Metzger, E., Mouret, A., Cesbron, F., Knoery, J.,
Rozuel, E., Launeau, P., Nardelli, M. P., Jorissen, F. J., and Geslin, E.:
Two-dimensional distribution of living benthic foraminifera in anoxic
sediment layers of an estuarine mudflat (Loire estuary, France),
Biogeosciences, 12, 6219–6234, <ext-link xlink:href="http://dx.doi.org/10.5194/bg-12-6219-2015" ext-link-type="DOI">10.5194/bg-12-6219-2015</ext-link>, 2015.</mixed-citation></ref>
      <ref id="bib1.bib63"><label>63</label><mixed-citation>
Trench, R. K., Trench, M. E., and Muscatin, L.: Symbiotic chloroplasts; their
photosynthetic products and contribution to mucus synthesis in two marine
slugs, Biol. Bull., 142, 335–349, 1972.</mixed-citation></ref>
      <ref id="bib1.bib64"><label>64</label><mixed-citation>Tsuchiya, M., Toyofuku, T., Uematsu, K., Brüchert, V., Collen, J.,
Yamamoto, H., and Kitazato, H.: Cytologic and genetic characteristics of
endobiotic bacteria and kleptoplasts of <italic>Virgulinella fragilis</italic>
(Foraminifera), J. Eukaryot. Microbiol., 62, 454–469, 2015.</mixed-citation></ref>
      <ref id="bib1.bib65"><label>65</label><mixed-citation>
Tyystjärvi, E. and Aro, E. M.: The rate constant of photoinhibition,
measured in lincomycin-treated leaves, is directly proportional to light
intensity, P. Natl. Acad. Sci. USA, 93, 2213–2218, 1996.</mixed-citation></ref>
      <ref id="bib1.bib66"><label>66</label><mixed-citation>Ventura, P., Calado, G., and Jesus, B.: Photosynthetic efficiency and
kleptoplast pigment diversity in the sea slug <italic>Thuridilla hopei</italic>
(Verany, 1853), J. Exp. Mar. Biol. Ecol., 441, 105–109, 2013.</mixed-citation></ref>
      <ref id="bib1.bib67"><label>67</label><mixed-citation>Vieira, S., Calado, R., Coelho, H., and Serodio, J.: Effects of light
exposure on the retention of kleptoplastic photosynthetic activity in the
sacoglossan mollusc <italic>Elysia viridis</italic>, Mar. Biol., 156, 1007–1020,
2009.</mixed-citation></ref>
      <ref id="bib1.bib68"><label>68</label><mixed-citation>
Yamaguchi, K., Mayfield, S., and Sugita, M.: Transcriptional and
Translational Regulation of Photosystem II Gene Expression, in: Photosystem
II, edited by: Wydrzynski, T., Satoh, K., and Freeman, J., Springer, the
Netherlands, 649–668, 2005.</mixed-citation></ref>

  </ref-list><app-group content-type="float"><app><title/>

    </app></app-group></back>
    <!--<article-title-html>Effect of light on photosynthetic efficiency of sequestered chloroplasts in
intertidal benthic foraminifera (<i>Haynesina germanica</i> and <i>Ammonia tepida</i>)</article-title-html>
<abstract-html><p class="p">Some benthic foraminifera have the ability to incorporate functional
chloroplasts from diatoms (kleptoplasty). Our objective was to investigate
chloroplast functionality of two benthic foraminifera (<i>Haynesina germanica</i> and <i>Ammonia tepida</i>) exposed to
different irradiance levels (0, 25, 70 µmol photon m<sup>−2</sup> s<sup>−1</sup>)
using spectral reflectance, epifluorescence observations, oxygen evolution
and pulse amplitude modulated (PAM) fluorometry (maximum photosystem II
quantum efficiency (Fv/Fm) and rapid light curves (RLC)). Our results clearly
showed that <i>H. germanica</i> was capable of using its kleptoplasts for more than 1 week
while <i>A. tepida</i> showed very limited kleptoplastic ability with  maximum photosystem II
quantum efficiency (Fv/Fm  =  0.4), much lower than <i>H. germanica</i> and decreasing to zero in only
1 day. Only <i>H. germanica</i> showed net oxygen production with a compensation point at 24 µmol photon m<sup>−2</sup> s<sup>−1</sup>
and a production up to 1000 pmol O<sub>2</sub> cell<sup>−1</sup> day<sup>−1</sup> at 300 µmol photon m<sup>−2</sup> s<sup>−1</sup>.
<i>Haynesina germanica</i> Fv/Fm slowly decreased from 0.65 to 0.55 in 7 days when kept in darkness;
however, it quickly decreased to 0.2 under high light. Kleptoplast
functional time was thus estimated between 11 and 21 days in darkness and
between 7 and 8 days at high light. These results emphasize that studies
about foraminifera kleptoplasty must take into account light history.
Additionally, this study showed that the kleptoplasts are unlikely to be
completely functional, thus requiring continuous chloroplast resupply from
foraminifera food source. The advantages of keeping functional chloroplasts
are discussed but more information is needed to better understand
foraminifera feeding strategies.</p></abstract-html>
<ref-html id="bib1.bib1"><label>1</label><mixed-citation>
Alve, E. and Murray, J. W.: Temporal variability in vertical distributions of
live (stained) intertidal foraminifera, southern England, J. Foramin.
Res., 31, 12–24, 2001.
</mixed-citation></ref-html>
<ref-html id="bib1.bib2"><label>2</label><mixed-citation>
Austin, H. A., Austin, W. E., and Paterson, D. M.: Extracellular cracking and
content removal of the benthic diatom <i>Pleurosigma angulatum</i> (Quekett) by the benthic foraminifera
<i>Haynesina germanica</i> (Ehrenberg), Mar. Micropaleontol., 57, 68–73, 2005.
</mixed-citation></ref-html>
<ref-html id="bib1.bib3"><label>3</label><mixed-citation>
Bernhard, J. M. and Bowser, S. S.: Benthic foraminifera of dysoxic sediments:
chloroplast sequestration and functional morphology, Earth-Sci. Rev., 46,
149–165, 1999.
</mixed-citation></ref-html>
<ref-html id="bib1.bib4"><label>4</label><mixed-citation>
Bouchet, V. M. P., Debenay, J.-P., Sauriau, P.-G., Radford-Knoery, J., and
Soletchnik, P.: Effects of short-term environmental disturbances on living
benthic foraminifera during the Pacific oyster summer mortality in the
Marennes-Oleron Bay (France), Mar. Environ. Res., 64, 358–383, 2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib5"><label>5</label><mixed-citation>
Bouchet, V. M. P., Sauriau, P.-G., Debenay, J.-P., Mermillod-Blondin, F.,
Schmidt, S., Amiard, J.-C., and Dupas, B.: Influence of the mode of
macrofauna-mediated bioturbation on the vertical distribution of living
benthic foraminifera: First insight from axial tomodensitometry, J. Exp.
Mar. Biol. Ecol., 371, 20–33, 2009.
</mixed-citation></ref-html>
<ref-html id="bib1.bib6"><label>6</label><mixed-citation>
Brotas, V. and Catarino, F.: Microphytobenthos primary production of Tagus
estuary intertidal flats (Portugal), Neth. J. Aquat. Ecol., 29, 333–339,
1995.
</mixed-citation></ref-html>
<ref-html id="bib1.bib7"><label>7</label><mixed-citation>
Cartaxana, P., Ruivo, M., Hubas, C., Davidson, I., Serôdio, J., and
Jesus, B.: Physiological versus behavioral photoprotection in intertidal
epipelic and epipsammic benthic diatom communities, J. Exp. Mar. Biol. Ecol.,
405, 120–127, 2011.
</mixed-citation></ref-html>
<ref-html id="bib1.bib8"><label>8</label><mixed-citation>
Cartaxana, P., Domingues, N., Cruz, S., Jesus, B., Laviale, M., Serôdio,
J., and Marques da Silva, J.: Photoinhibition in benthic diatom assemblages
under light stress, Aquat. Microb. Ecol., 70, 87–92, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib9"><label>9</label><mixed-citation>
Campbell, D. A.  and Tyystjarvi, E.: Parameterization of photosystem II
photoinactivation and repair, BBA-Bioenergetics, 1817,
258–265, 2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib10"><label>10</label><mixed-citation>
Cesbron, F., Geslin, E., Jorissen, F. J., Delgard, M. L., Charrieau, L.,
Deflandre, B., Jézéquel, D., Anschutz, P., and Metzger, E.: Vertical distribution
and respiration rates of benthic foraminifera: Contribution to aerobic
remineralization in intertidal mudflats covered by <i>Zostera noltei</i> meadows, Estuar. Coast.
Shelf S., in press, 2016.
</mixed-citation></ref-html>
<ref-html id="bib1.bib11"><label>11</label><mixed-citation>
Clark, K. B., Jensen, K. R., and Stirts, H. M.: Survey for functional
kleptoplasty among West Atlantic Ascoglossa ( = Sacoglossa) (Mollusca:
Opisthobranchia), Veliger, 33, 339–345, 1990.
</mixed-citation></ref-html>
<ref-html id="bib1.bib12"><label>12</label><mixed-citation>
Correia, M. J. and Lee, J. J.: Chloroplast retention by <i>Elphidium excavatum</i> (Terquem). Is it a
selective process?, Symbiosis, 29, 343–355, 2000.
</mixed-citation></ref-html>
<ref-html id="bib1.bib13"><label>13</label><mixed-citation>
Correia, M. J. and Lee, J. J.: Fine structure of the plastids retained by the
foraminifer <i>Elphidium excavatum</i> (Terquem), Symbiosis, 32,  15–26, 2002a.
</mixed-citation></ref-html>
<ref-html id="bib1.bib14"><label>14</label><mixed-citation>
Correia, M. J. and Lee, J. J.: How long do the plastids retained by <i>Elphidium excavatum</i> (Terquem)
last in their host?, Symbiosis, 32, 27–37, 2002b.
</mixed-citation></ref-html>
<ref-html id="bib1.bib15"><label>15</label><mixed-citation>
Costa, J., Gimenez-Casalduero, F., Melo, R., and  Jesus, B.: Colour morphotypes
of <i>Elysia timida</i> (Sacoglossa, Gastropoda) are determined by light acclimation in food
algae, Aquat. Biol., 17, 81–89, 2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib16"><label>16</label><mixed-citation>
Curtis, N. E., Middlebrooks, M. L., Schwartz, J. A., and Pierce, S. K.: PAM
analysis of 3 sacoglossan species reveals differences in photosynthetic
function and chloroplast longevity, Integr. Comp. Biol., 53, 272–272, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib17"><label>17</label><mixed-citation>
Debenay, J.-P., Guillou, J.-J., Redois, F., and Geslin, E.: Distribution
trends of foraminiferal assemblages in paralic environments, in:
Environmental Micropaleontology, edited by: Martin, R. E., Springer
US, New York, 39–67, 2000.
</mixed-citation></ref-html>
<ref-html id="bib1.bib18"><label>18</label><mixed-citation>
Debenay, J. P., Bicchi, E., Goubert, E., and du Chatelet, E. A.:
Spatio-temporal distribution of benthic foraminifera in relation to estuarine
dynamics (Vie estuary, Vendee, W France), Estuar. Coast. Shelf S., 67,
181–197, 2006.
</mixed-citation></ref-html>
<ref-html id="bib1.bib19"><label>19</label><mixed-citation>
Eberhard, S., Finazzi, G., and Wollman, F.-A.: The dynamics of
photosynthesis, Annu. Rev. Genet., 42,   463–515, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib20"><label>20</label><mixed-citation>
Evertsen, J., Burghardt, I., Johnsen, G., and Wagele, H.: Retention of
functional chloroplasts in some sacoglossans from the Indo-Pacific and
Mediterranean, Mar. Biol., 151, 2159–2166, 2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib21"><label>21</label><mixed-citation>
Falkowski, P. G. and Raven, J. A.: Aquatic photosynthesis, second Edn.,
Princeton Universty Press, Princeton, 2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib22"><label>22</label><mixed-citation>
Geslin, E., Risgaard-Petersen, N., Lombard, F., Metzger, E., Langlet, D., and
Jorissen, F.: Oxygen respiration rates of benthic foraminifera as measured
with oxygen microsensors, J. Exp. Mar. Biol. Ecol., 396, 108–114, 2011.
</mixed-citation></ref-html>
<ref-html id="bib1.bib23"><label>23</label><mixed-citation>
Goldstein, S. T., Habura, A., Richardson, E. A., and Bowser, S. S.:
<i>Xiphophaga minuta</i>, and <i>X. allominuta</i>, nov. gen., nov. spp.,
new monothalamid Foraminifera from coastal Georgia (USA): cryptic species,
gametogenesis, and an unusual form of chloroplast sequestration, J. Foramin.
Res., 40, 3–15, 2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib24"><label>24</label><mixed-citation>
Goldstein, S. T., Bernhard, J. M., and Richardson, E. A. Chloroplast
sequestration in the foraminifer <i>Haynesina germanica</i>: Application of
high pressure freezing and freeze substitution, Microsc. Microanal., 10,
1458–1459, 2004.
</mixed-citation></ref-html>
<ref-html id="bib1.bib25"><label>25</label><mixed-citation>
Gooday, A. J.: Meiofaunal foraminiferans from the bathyal Porcupine Seabight
(northeast Atlantic): size structure, standing stock, taxonomy composition,
species diversity and vertical distribution in the sediment, Deep-Sea Res.
Pt. I, 33, 1345–1373, 1986.
</mixed-citation></ref-html>
<ref-html id="bib1.bib26"><label>26</label><mixed-citation>
Green, B. J., Li, W.-Y., Manhart, J. R., Fox, T. C., Summer, E. J., Kennedy, R. A.,
Pierce, S. K., and Rumpho, M. E.: Mollusc-algal chloroplast endosymbiosis.
Photosynthesis, thylakoid protein maintenance, and chloroplast gene
expression continue for many months in the absence of the algal nucleus,
Plant Physiol., 124, 331–342, 2001.
</mixed-citation></ref-html>
<ref-html id="bib1.bib27"><label>27</label><mixed-citation>
Gross, O.: Influence of temperature, oxygen and food availability on the
migrational activity of bathyal benthic foraminifera: evidence by microcosm
experiments, Hydrobiologia, 426, 123–137, 2000.
</mixed-citation></ref-html>
<ref-html id="bib1.bib28"><label>28</label><mixed-citation>
Grzymski, J., Schofield, O. M., Falkowski, P. G., and Bernhard, J. M.: The
function of plastids in the deep-sea benthic foraminifer, <i>Nonionella stella</i>, Limnol.
Oceanogr., 47, 1569–1580, 2002.
</mixed-citation></ref-html>
<ref-html id="bib1.bib29"><label>29</label><mixed-citation>
Hannah, F., Rogerson, A., and Laybournparry, J.: Respiration rates and
biovolumes of common benthic foraminifera (Protozoa), J. Mar. Biol. Assoc.
UK, 74, 301–312, 1994.
</mixed-citation></ref-html>
<ref-html id="bib1.bib30"><label>30</label><mixed-citation>
Hayward, B. W., Holzmann, M., Grenfell, H. R., Pawlowski, J., and Triggs, C. M.:
Morphological distinction of molecular types in Ammonia – towards a
taxonomic revision of the world's most commonly misidentified foraminifera,
Mar. Micropaleontol., 50, 237–271, 2004.
</mixed-citation></ref-html>
<ref-html id="bib1.bib31"><label>31</label><mixed-citation>
Høgslund, S., Revsbech, N. P., Cedhagen, T., Nielsen, L. P., and Gallardo,
V. A.: Denitrification, nitrate turnover, and aerobic respiration by benthic
foraminiferans in the oxygen minimum zone off Chile, J. Exp. Mar. Biol.
Ecol., 359, 85–91, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib32"><label>32</label><mixed-citation>
Jesus, B., Perkins, R. G., Consalvey, M., Brotas, V., and Paterson, D. M.:
Effects of vertical migrations by benthic microalgae on fluorescence
measurements of photophysiology, Mar. Ecol.-Prog. Ser., 315, 55–66, 2006.
</mixed-citation></ref-html>
<ref-html id="bib1.bib33"><label>33</label><mixed-citation>
Jesus, B., Mouget, J.-L., and Perkins, R. G.: Detection of diatom xanthophyll
cycle using spectral reflectance, J. Phycol., 44, 1349–1359, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib34"><label>34</label><mixed-citation>
Jesus, B., Brotas, V., Ribeiro, L., Mendes, C. R., Cartaxana, P., and
Paterson, D. M.: Adaptations of microphytobenthos assemblages to sediment
type and tidal position, Cont. Shelf Res., 29, 1624–1634, 2009.
</mixed-citation></ref-html>
<ref-html id="bib1.bib35"><label>35</label><mixed-citation>
Jesus, B., Ventura, P., and Calado, G.: Behaviour and a functional
xanthophyll cycle enhance photo-regulation mechanisms in the solar-powered
sea slug <i>Elysia timida</i> (Risso, 1818), J. Exp. Mar. Biol. Ecol., 395, 98–105,
2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib36"><label>36</label><mixed-citation>
Kazemipour, F., Launeau, P., and Méléder, V.: Microphytobenthos
biomass mapping using the optical model of diatom biofilms: Application to
hyperspectral images of Bourgneuf Bay, Remote Sens. Environ., 127, 1–13,
2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib37"><label>37</label><mixed-citation>
Knight, R. and Mantoura, R. F. C.: Chlorophyll and carotenoid pigments in
foraminifera and their symbiotic algae: analysis by high performance liquid
chromatography, Mar. Ecol.-Prog. Ser., 23, 241–249, 1985.
</mixed-citation></ref-html>
<ref-html id="bib1.bib38"><label>38</label><mixed-citation>
Lee, J. J., Lanners, E., and Ter Kuile, B.: The retention of chloroplasts by
the foraminifera <i>Elphidium crispum</i>, Symbiosis, 5, 45–60, 1988.
</mixed-citation></ref-html>
<ref-html id="bib1.bib39"><label>39</label><mixed-citation>
Li, Y. H. and Gregory, S.: Diffusion of ions in sea-water and deep-sea
sediments, Geochim. Cosmochim. Ac., 38, 703–714, 1974.
</mixed-citation></ref-html>
<ref-html id="bib1.bib40"><label>40</label><mixed-citation>
Lopez, E.: Algal chloroplasts in the protoplasm of three species of benthic
foraminifera: taxonomic affinity, viability and persistence, Mar. Biol., 53,
201–211, 1979.
</mixed-citation></ref-html>
<ref-html id="bib1.bib41"><label>41</label><mixed-citation>
MacIntyre, H. L., Geider, R. J., and Miller, D. C.: Microphytobenthos: The
ecological role of the “secret garden” of unvegetated, shallow-water
marine habitats .1. Distribution, abundance and primary production,
Estuaries, 19, 186–201, 1996.
</mixed-citation></ref-html>
<ref-html id="bib1.bib42"><label>42</label><mixed-citation>
Marchetti, J., Bougaran, G., Jauffrais, T., Lefebvre, S., Rouxel, C.,
Saint-Jean, B., Lukomska, E., Robert, R., and Cadoret, J. P.: Effects of blue
light on the biochemical composition and photosynthetic activity of
<i>Isochrysis</i> sp. (T-iso), J. Appl. Phycol., 25, 109–119, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib43"><label>43</label><mixed-citation>
Meleder, V., Barille, L., Launeau, P., Carrere, V., and Rince, Y.:
Spectrometric constraint in analysis of benthic diatom biomass using
monospecific cultures, Remote Sens. Environ., 88, 386–400, 2003.
</mixed-citation></ref-html>
<ref-html id="bib1.bib44"><label>44</label><mixed-citation>
Meleder, V., Laviale, M., Jesus, B., Mouget, J. L., Lavaud, J., Kazemipour,
F., Launeau, P., and Barille, L.: In vivo estimation of pigment composition
and optical absorption cross-section by spectroradiometry in four aquatic
photosynthetic micro-organisms, J. Photoch. Photobio. B, 129,
115–124, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib45"><label>45</label><mixed-citation>
Moodley, L., Middelburg, J. J., Boschker, H. T. S., Duineveld, G. C. A., Pel, R.,
Herman, P. M. J., and Heip, C. H. R.: Bacteria and Foraminifera: key players in a
short-term deep-sea benthic response to phytodetritus, Mar. Ecol.-Prog. Ser.,
236:, 23–29, 2002.
</mixed-citation></ref-html>
<ref-html id="bib1.bib46"><label>46</label><mixed-citation>
Morvan, J., Debenay, J.-P., Jorissen, F., Redois, F., Beneteau, E.,
Delplancke, M., and Amato, A.-S. Patchiness and life cycle of intertidal
foraminifera: Implication for environmental and paleoenvironmental
interpretation, Mar. Micropaleontol., 61, 131–154, 2006.
</mixed-citation></ref-html>
<ref-html id="bib1.bib47"><label>47</label><mixed-citation>
Mouget, J.-L., Perkins, R. G., Consalvey, M., and Lefebvre, S.: Migration or
photoacclimation to prevent photoinhibition and UV-B damage in marine
microphytobenthic communities, Aquat. Microb. Ecol., 52, 223–232, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib48"><label>48</label><mixed-citation>
Papacek, S., Celikovsky, S., Rehak, B., and Stys, D.: Experimental design for
parameter estimation of two time-scale model of photosynthesis and
photoinhibition in microalgae, Math. Comput. Simulat., 80, 1302–1309, 2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib49"><label>49</label><mixed-citation>
Pascal, P.-Y., Dupuy, C., Richard, P., Mallet, C., du Chatelet, E. A., and
Niquil, N.: Seasonal variation in consumption of benthic bacteria by meio-
and macrofauna in an intertidal mudflat, Limnol. Oceanogr., 54, 1048–1059,
2009.
</mixed-citation></ref-html>
<ref-html id="bib1.bib50"><label>50</label><mixed-citation>
Perkins, R. G., Underwood, G. J. C., Brotas, V., Snow, G. C., Jesus, B., and
Ribeiro, L.: Responses of microphytobenthos to light: primary production and
carbohydrate allocation over an emersion period, Mar. Ecol.-Prog. Ser., 223,
101–112, 2001.
</mixed-citation></ref-html>
<ref-html id="bib1.bib51"><label>51</label><mixed-citation>
Perkins, R. G., Mouget, J.-L., Lefebvre, S., and Lavaud, J.: Light response
curve methodology and possible implications in the application of chlorophyll
fluorescence to benthic diatoms, Mar. Biol., 149, 703–712, 2006.
</mixed-citation></ref-html>
<ref-html id="bib1.bib52"><label>52</label><mixed-citation>
Perkins, R. G., Lavaud, J., Serodio, J., Mouget, J. L., Cartaxana, P., Rosa,
P., Barille, L., Brotas, V., and Jesus, B. M.: Vertical cell movement is a
primary response of intertidal benthic biofilms to increasing light dose,
Mar. Ecol.-Prog. Ser., 416, 93–103, 2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib53"><label>53</label><mixed-citation>
Pillet, L. and Pawlowski, J.: Transcriptome analysis of foraminiferan
<i>Elphidium margaritaceum</i> questions the role of gene transfer in
kleptoplastidy, Mol. Biol. Evol., 30, 66–69, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib54"><label>54</label><mixed-citation>
Pillet, L., de Vargas, C., and Pawlowski, J.: Molecular identification of
sequestered diatom chloroplasts and kleptoplastidy in foraminifera, Protist,
162, 394–404, 2011.
</mixed-citation></ref-html>
<ref-html id="bib1.bib55"><label>55</label><mixed-citation>
Pina-Ochoa, E., Hogslund, S., Geslin, E., Cedhagen, T., Revsbech, N. P., Nielsen, L. P., Schweizer, M., Jorissen, F., Rysgaard, S., and Risgaard-Petersen, N.: Widespread occurrence
of nitrate storage and denitrification among foraminifera and gromiida,
P. Natl. Acad. Sci. USA, 107, 1148–1153, 2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib56"><label>56</label><mixed-citation>
Platt, T., Gallegos, C. L., and Harrison, W. G.: Photoinhibition of
photosynthesis in natural assemblages of marine phytoplankton, J. Mar. Res.,
38, 687–701, 1980.
</mixed-citation></ref-html>
<ref-html id="bib1.bib57"><label>57</label><mixed-citation>
Revsbech, N. P.: An oxygen microsensor with a guard cathode, Limnol.
Oceanogr., 34, 474–478, 1989.
</mixed-citation></ref-html>
<ref-html id="bib1.bib58"><label>58</label><mixed-citation>
Rink, S., Kuhl, M., Bijma, J., and Spero, H. J.: Microsensor studies of
photosynthesis and respiration in the symbiotic foraminifer <i>Orbulina universa</i>, Mar.
Biol., 131, 583–595, 1998.
</mixed-citation></ref-html>
<ref-html id="bib1.bib59"><label>59</label><mixed-citation>
Risgaard-Petersen, N., Langezaal, A. M., Ingvardsen, S., Schmid, M. C.,
Jetten, M. S. M., Op den Camp, H. J. M., Derksen, J. W. M., Pina-Ochoa, E.,
Eriksson, S. P., Nielsen, L. P., Revsbech, N. P., Cedhagen, T., and van der
Zwaan, G. J.: Evidence for complete denitrification in a benthic foraminifer,
Nature, 443, 93–96, 2006.
</mixed-citation></ref-html>
<ref-html id="bib1.bib60"><label>60</label><mixed-citation>
Rumpho, M. E., Summer, E. J., Green, B. J., Fox, T. C., and Manhart, J. R.:
Mollusc/algal chloroplast symbiosis: how can isolated chloroplasts continue
to function for months in the cytosol of a sea slug in the absence of an
algal nucleus?, Zoology, 104, 303–312, 2001.

</mixed-citation></ref-html>
<ref-html id="bib1.bib61"><label>61</label><mixed-citation>
Serodio, J., Pereira, S., Furtado, J., Silva, R., Coelho, H., and Calado, R.:
In vivo quantification of kleptoplastic chlorophyll a content in the
“solar-powered” sea slug <i>Elysia viridis</i> using optical methods:
spectral reflectance analysis and PAM fluorometry, Photochem. Photobio. S.,
9, 68–77, 2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib62"><label>62</label><mixed-citation>
Thibault de Chanvalon, A., Metzger, E., Mouret, A., Cesbron, F., Knoery, J.,
Rozuel, E., Launeau, P., Nardelli, M. P., Jorissen, F. J., and Geslin, E.:
Two-dimensional distribution of living benthic foraminifera in anoxic
sediment layers of an estuarine mudflat (Loire estuary, France),
Biogeosciences, 12, 6219–6234, <a href="http://dx.doi.org/10.5194/bg-12-6219-2015" target="_blank">doi:10.5194/bg-12-6219-2015</a>, 2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib63"><label>63</label><mixed-citation>
Trench, R. K., Trench, M. E., and Muscatin, L.: Symbiotic chloroplasts; their
photosynthetic products and contribution to mucus synthesis in two marine
slugs, Biol. Bull., 142, 335–349, 1972.
</mixed-citation></ref-html>
<ref-html id="bib1.bib64"><label>64</label><mixed-citation>
Tsuchiya, M., Toyofuku, T., Uematsu, K., Brüchert, V., Collen, J.,
Yamamoto, H., and Kitazato, H.: Cytologic and genetic characteristics of
endobiotic bacteria and kleptoplasts of <i>Virgulinella fragilis</i>
(Foraminifera), J. Eukaryot. Microbiol., 62, 454–469, 2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib65"><label>65</label><mixed-citation>
Tyystjärvi, E. and Aro, E. M.: The rate constant of photoinhibition,
measured in lincomycin-treated leaves, is directly proportional to light
intensity, P. Natl. Acad. Sci. USA, 93, 2213–2218, 1996.
</mixed-citation></ref-html>
<ref-html id="bib1.bib66"><label>66</label><mixed-citation>
Ventura, P., Calado, G., and Jesus, B.: Photosynthetic efficiency and
kleptoplast pigment diversity in the sea slug <i>Thuridilla hopei</i>
(Verany, 1853), J. Exp. Mar. Biol. Ecol., 441, 105–109, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib67"><label>67</label><mixed-citation>
Vieira, S., Calado, R., Coelho, H., and Serodio, J.: Effects of light
exposure on the retention of kleptoplastic photosynthetic activity in the
sacoglossan mollusc <i>Elysia viridis</i>, Mar. Biol., 156, 1007–1020,
2009.
</mixed-citation></ref-html>
<ref-html id="bib1.bib68"><label>68</label><mixed-citation>
Yamaguchi, K., Mayfield, S., and Sugita, M.: Transcriptional and
Translational Regulation of Photosystem II Gene Expression, in: Photosystem
II, edited by: Wydrzynski, T., Satoh, K., and Freeman, J., Springer, the
Netherlands, 649–668, 2005.
</mixed-citation></ref-html>--></article>
