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  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">BG</journal-id>
<journal-title-group>
<journal-title>Biogeosciences</journal-title>
<abbrev-journal-title abbrev-type="publisher">BG</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Biogeosciences</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1726-4189</issn>
<publisher><publisher-name>Copernicus Publications</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/bg-13-4187-2016</article-id><title-group><article-title>Mechanisms of <italic>Trichodesmium</italic> demise within the New Caledonian lagoon during the VAHINE
mesocosm experiment</article-title>
      </title-group><?xmltex \runningtitle{Mechanisms of \textit{Trichodesmium} demise within the New Caledonian lagoon}?><?xmltex \runningauthor{D.~Spungin et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Spungin</surname><given-names>Dina</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Pfreundt</surname><given-names>Ulrike</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Berthelot</surname><given-names>Hugo</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3 aff4">
          <name><surname>Bonnet</surname><given-names>Sophie</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>AlRoumi</surname><given-names>Dina</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Natale</surname><given-names>Frank</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Hess</surname><given-names>Wolfgang R.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Bidle</surname><given-names>Kay D.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Berman-Frank</surname><given-names>Ilana</given-names></name>
          <email>ilana.berman-frank@biu.ac.il</email>
        <ext-link>https://orcid.org/0000-0003-3497-1844</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>The Mina and Everard Goodman Faculty of Life Sciences,
Bar-Ilan University, Ramat-Gan, Israel</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>University of Freiburg, Faculty of Biology,
Schänzlestr. 1, 79104 Freiburg, Germany</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Aix Marseille Université, CNRS/INSU, Université
de Toulon, IRD, Mediterranean Institute of Oceanography (MIO)<?xmltex \hack{\newline}?> UM 110, 13288,
Marseille, France</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Institut de Recherche pour le Développement (IRD),
AMU/CNRS/INSU, Université de Toulon, Mediterranean<?xmltex \hack{\newline}?> Institute of
Oceanography (MIO) UM 110, 13288, Noumea, New
Caledonia</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>Department of Marine and Coastal Sciences, Rutgers
University, New Brunswick, NJ, USA</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Ilana Berman-Frank (ilana.berman-frank@biu.ac.il)</corresp></author-notes><pub-date><day>22</day><month>July</month><year>2016</year></pub-date>
      
      <volume>13</volume>
      <issue>14</issue>
      <fpage>4187</fpage><lpage>4203</lpage>
      <history>
        <date date-type="received"><day>7</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>28</day><month>May</month><year>2016</year></date>
           <date date-type="accepted"><day>17</day><month>June</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/13/4187/2016/bg-13-4187-2016.html">This article is available from https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016.html</self-uri>
<self-uri xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016.pdf</self-uri>


      <abstract>
    <p>The globally important marine diazotrophic cyanobacterium
<italic>Trichodesmium</italic> is abundant in the New Caledonian lagoon (southwestern
Pacific Ocean) during austral spring/summer. We investigated the cellular
processes mediating <italic>Trichodesmium</italic> mortality from large surface
accumulations (blooms) in the lagoon. <italic>Trichodesmium</italic> cells (and
associated microbiota) were collected at the time of surface accumulation,
enclosed under simulated ambient conditions, and sampled over time to
elucidate the stressors and subcellular underpinning of rapid biomass demise
(&gt; 90 % biomass crashed within <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 24 h).
Metatranscriptomic profiling of <italic>Trichodesmium</italic> biomass, 0, 8 and
22 h after incubations of surface accumulations, demonstrated upregulated
expression of genes required to increase phosphorus (P) and iron (Fe)
availability and transport, while genes responsible for nutrient storage were
downregulated. Total viral abundance oscillated throughout the experiment and
showed no significant relationship with the development or demise of the
<italic>Trichodesmium</italic> biomass. Enhanced caspase-specific activity and
upregulated expression of a suite of metacaspase genes, as the
<italic>Trichodesmium</italic> biomass crashed, implied autocatalytic programmed cell
death (PCD) as the mechanistic cause. Concurrently, genes associated with
buoyancy and gas vesicle production were strongly downregulated concomitant
with increased production and high concentrations of transparent exopolymeric
particles (TEP). The rapid, PCD-mediated, decline of the
<italic>Trichodesmium</italic> biomass, as we observed from our incubations,
parallels mortality rates reported from <italic>Trichodesmium</italic> blooms in
situ. Our results suggest that, whatever the ultimate factor, PCD-mediated
death in <italic>Trichodesmium</italic> can rapidly terminate blooms, facilitate
aggregation, and expedite vertical flux to depth.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>The filamentous N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixing (diazotrophic) cyanobacteria
<italic>Trichodesmium</italic> spp. are important contributors to marine N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fixation as they form massive blooms (surface accumulations with high biomass
density) throughout the oligotrophic marine subtropical and tropical oceans
(Capone et al., 1997, 2004; Capone and Carpenter, 1982). These surface blooms
with densities of 3000 to &gt; 10 000 trichomes L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (Chl <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>a</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> concentrations ranging from 1 to 5 mg L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
develop swiftly and are characterized by high rates of CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fixation (Capone et al., 1998; Luo et al., 2012; Rodier and Le Borgne, 2008,
2010). <italic>Trichodesmium</italic> blooms also occur frequently during austral
summer between November and March over large areas of the New Caledonian
lagoon in the southwestern Pacific Ocean (Dandonneau and Gohin, 1984; Dupouy et
al., 2011).</p>
      <p><italic>Trichodesmium</italic> has been extensively investigated (reviewed in Capone
et al., 1997; Bergman et al., 2012). However, relatively few publications
have examined the mortality and fate of these blooms that often collapse
abruptly with mortality rates paralleling growth rates and biomass declines
&gt; 50 % occurring within 24 h from peak abundance (Bergman et
al., 2012; Rodier and Le Borgne, 2008, 2010). Cell mortality can occur due to
grazing of <italic>Trichodesmium</italic> by pelagic harpacticoid copepods (O'Neil,
1998) or by viral lysis (Hewson et al., 2004; Ohki, 1999). Both iron (Fe) and
phosphorus (P) availability regulate N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fixation and production of
<italic>Trichodesmium</italic> populations, causing a variety of stress responses
when these nutrients are limited (Berman-Frank et al., 2001). Fe depletion,
or high light and associated
oxidative stress, can also induce in <italic>Trichodesmium</italic> a genetically
controlled programmed cell death (PCD) that occurs in both laboratory
cultures and in natural populations (Bar-Zeev et al., 2013; Berman-Frank et
al., 2004, 2007). Mortality of <italic>Trichodesmium</italic> via PCD is
morphologically and physiologically distinct from necrotic death and triggers
rapid sinking of biomass that could enhance carbon export in oligotrophic
environments (Bar-Zeev et al., 2013). Sinking is due to concomitant internal
cellular degradation, vacuole loss, and the increased production of
extracellular polysaccharide aggregates, operationally defined as transparent
exopolymeric particles (TEP) (Bar-Zeev et al., 2013, 2004; Berman-Frank et
al., 2007).</p>
      <p>The VAHINE project investigated the fate of newly fixed N by diazotrophs and
aimed to test changes in organic matter export, following diazotroph
development and mortality. For this, large (50 m<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> mesocosms were
deployed in the New Caledonian lagoon and followed over the course of
23 days (Bonnet et al., 2016a). Our objective during the VAHINE project was
to study the involvement of PCD in the fate of natural <italic>Trichodesmium</italic>
blooms induced in these mesocosms. While <italic>Trichodesmium</italic> was initially
present, and conditions in the mesocosms appeared favorable, no
<italic>Trichodesmium</italic> blooms developed within the mesocosms, yet UCYN-C did
increase, allowing for the scientific objectives of the project to be met
(Berthelot et al., 2015; Bonnet et al., 2016a; Turk-Kubo et al., 2015).
However, <italic>Trichodesmium</italic> developed at different phases of the
experimental period outside the mesocosms (Turk-Kubo et al., 2015). Here, we
investigated mortality processes in a short-lived<italic> Trichodesmium</italic>
bloom that developed and crashed in the lagoon waters at the end of the
VAHINE experiment. Using a series of microcosm incubations with collected
<italic>Trichodesmium</italic> biomass, we elucidated the stressors and subcellular
underpinning of rapid (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 24 h) biomass demise and disappearance. Here
we present physiological, biochemical, and
metatranscriptomic evidence for nutrient-stress-induced PCD in natural
populations that leads to <italic>Trichodesmium</italic> mortality, including
concomitant downregulation of gas vesicle synthesis and enhanced TEP
production. Such mechanisms would lead to enhanced export flux in natural
blooms that also crash within 1–2 days.</p>
</sec>
<sec id="Ch1.S2">
  <title>Methods</title>
<sec id="Ch1.S2.SS1">
  <title>Sampling site and sampling conditions during pre-bloom periods</title>
      <p>Our study was performed during the VAHINE mesocosm project set 28 km off the
coast of New Caledonia from 13 January 2013 (day 1) to 6 February 2013 in the
New Caledonian oligotrophic lagoon (22<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>29.10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> S,
166<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>26.90<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> E). The 25 m deep sandy-bottom lagoon is generally
protected from the dominant trade winds, yet the waters of the lagoon are
influenced by the oligotrophic oceanic waters coming into the lagoon via the
Boulari Pass (Bonnet et al., 2016a). Detailed descriptions of the site
selection and sampling strategy are provided elsewhere (Bonnet et al.,
2016a). The lagoon water outside the mesocosms was sampled daily during the
experiment and served as the source for “pre-bloom”
data. Throughout the study all noted hours are Noumea local times (LT). Every day, large-volume
samples (50 L) were collected from 1, 6, and 12 m depths at 07:00 LT using
a Teflon<sup>®</sup> PFA pump and PVC tubing. Samples
were immediately transferred back to laboratories aboard the R/V
<italic>Alis</italic> and subsampled for a suite of parameters (as described below
and in Bonnet et al., 2016a). On day 23 at 12:00, we observed a large surface
accumulation of <italic>Trichodesmium</italic> in the lagoon close to the enclosed
mesocosms. This biomass accumulation (hereafter called “bloom”) served as
the source for experiments 1 and 2 to examine the fate of
<italic>Trichodesmium</italic> (Sect. 2.2, Fig. S1 in Supplement).</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Short-term incubations to assess bloom decline</title>
      <p><italic>Experiment 1</italic> – <italic>Trichodesmium</italic> filaments and colonies were
collected from the dense surface bloom (day 23,
12:00; designated <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>,
Fig. 2a–c) using a plankton net (mesh size, 80 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m) towed through
different patches of the bloom from the surface water. The total contents of
the net were combined and resuspended in filtered seawater (FSW)
(0.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m pore size), split between six identical 4.5 L Nalgene
polycarbonate bottles (Fig. 2d–e), and incubated as detailed below. Based on
previous experience (Berman-Frank et al., 2004), resuspension of
<italic>Trichodesmium</italic> cells in the extremely high densities of the surface
blooms (&gt; 1 mg L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>; Fig. 2a–c) would cause an
almost immediate crash of the biomass. Consequently, we resuspended the
collected biomass in FSW at <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 1000-fold lower cell densities
(150 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> that resemble the cellular abundance at the
edges of the slicks (Fig. 2). <italic>Experiment 2</italic> – Seawater from the
surface bloom was collected 5 h after the initial surface bloom was sighted
(day 23, 17:00) by using a
Teflon<sup>®</sup> PFA pump and PVC tubing directly
filling nine 20 L polyethylene carboys gently to avoid destroying biomass.
Bottles from experiments 1 and 2 were placed in on-deck incubators, filled
with running seawater to maintain ambient surface temperature
(<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 26 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C), and covered with neutral screening at 50 %
surface irradiance levels. Water from experiment 1 was sampled every 2–4 h
for Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentration, caspase activity, 16S rRNA gene sequencing, and
metatranscriptomics until the biomass collapsed (after <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula>22 h). Water
from experiment 2 was sampled for PON, POC, NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation
rates, TEP production, and virus abundance (days 23–25) (Fig. S1). Prior to
incubations, all incubation bottles and carboys were washed with 10 % HCl
overnight and rinsed three times with ambient seawater.</p>
</sec>
<sec id="Ch1.S2.SS3">
  <?xmltex \opttitle{Chlorophyll~$a$ concentrations}?><title>Chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations</title>
      <p>Samples for the determination of Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations during pre-bloom days
were collected by filtering 550 mL of seawater on GF/F filters (Whatman, Kent, UK). Filters were
snap-frozen and stored in liquid nitrogen. Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> was extracted in methanol and
measured fluorometrically (Herbland et al., 1985), and in experiment 1 measured spectrophotometrically (664 and 750 nm; CARY100, Varian, Santa Clara, CA,
USA) according to Tandeau de Marsac and Houmard (1988).</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Particulate organic carbon (POC) and nitrogen (PON)</title>
      <p>Detailed POC and PON analyses are described in Berthelot et al. (2015). POC
samples were collected by filtering 2.3 L of seawater through precombusted
(450 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, 4 h) GF/F filter and determined using the combustion
method (Strickland and Parsons, 1972) on an EA 2400 CHN analyzer. Samples for
PON concentrations were collected by filtering 1.2 L of water on
precombusted (450 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, 4 h) and acid-washed (HCl, 10 %) GF/F
filters and analyzed according to the wet oxidation protocol described in
Pujo-Pay and Raimbault (1994) with a precision of
0.06 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <?xmltex \opttitle{N${}_{{2}}$-fixation rates and NH${}_{{4}}{}^{{+}}$ concentrations}?><title>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rates and NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations</title>
      <p>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rate measurements used in experiment 2 are described in
detail in Berthelot et al. (2015). Samples were collected at
17:00 in 4.5 L polycarbonate bottles and amended
with <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-enriched seawater, within an hour of biomass collection,
according to the protocol developed by Mohr et al. (2010) and Rahav et
al. (2013). Briefly, seawater was degassed through a degassing membrane
(Membrana, Minimodule<sup>®</sup>, flow rate fixed at
450 mL min<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> connected to a vacuum pump. Degassed seawater was
amended with 1 mL of <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (98.9 % atom <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N, Cambridge
Isotopes) per 100 mL. The bottle was shaken vigorously and incubated
overnight at 3 bar to promote <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> dissolution. Incubation
bottles were amended with <inline-formula><mml:math display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>:</mml:mo><mml:mn>20</mml:mn></mml:mrow></mml:math></inline-formula> (vol : vol) of <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-enriched
seawater, closed without headspace with silicone septum caps, and incubated
for 24 h under in situ-simulated conditions in on-deck incubators
(described above). A total of 2.2 L from each experimental bottle was filtered under
low vacuum pressure (&lt; 100 mm Hg) onto a precombusted
(450 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, 4 h) GF/F filter (25 mm diameter, 0.7 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m
nominal porosity). The filters were stored at <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>20 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C and dried for
24 h at 60 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C before mass spectrometric analysis. PON content and
PON <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N enrichments were determined using a Thermo Fisher
Scientific Delta Plus isotope ratio mass spectrometer (Bremen, Germany) coupled with an
elemental analyzer (Flash EA, Thermo Fisher Scientific). N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation
rates were calculated according to the equations detailed in Montoya et
al. (1996). We assumed significant rates when the <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N enrichment of the
PON was higher than 3 times the standard deviation obtained from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
samples. The <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn>15</mml:mn></mml:msup></mml:math></inline-formula>N batch did not indicate that our results were
overestimated by contamination of the spike solution (Berthelot et al.,
2015).</p>
      <p>Samples for NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> were collected in 40 mL glass vials and analyzed by
the fluorescence method according to Holmes et al. (1999), using a Trilogy
fluorometer (Turner Design).</p>
</sec>
<sec id="Ch1.S2.SS6">
  <title>Transparent exopolymeric particles (TEP)</title>
      <p>Water samples (100 mL) were gently (&lt; 150 mbar) filtered through a
0.45 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m polycarbonate filter (GE Water &amp; Process Technologies).
Filters were then stained with a solution of 0.02 % Alcian blue (AB) and
0.06 % acetic acid (pH of 2.5), and the excess dye was removed by a quick
deionized water rinse. Filters were then immersed in sulfuric acid (80 %)
for 2 h, and the absorbance (787 nm) was measured spectrophotometrically
(CARY 100, Varian). AB was calibrated using a purified polysaccharide gum
xanthan (GX) (Passow and Alldredge, 1995). TEP concentrations (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX
equivalents L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> were measured according to Passow and Alldredge (1995).</p>
</sec>
<sec id="Ch1.S2.SS7">
  <title>Virus abundance</title>
      <p>Total seawater (1 mL) was fixed with 0.5 % glutaraldehyde and
snap-frozen in liquid nitrogen until processed. Flow cytometry was conducted
using an Influx model 209S Mariner flow cytometer and high-speed cell sorter
equipped with a 488 nm 200 mW blue laser and two scatter, two polarized,
and four fluorescence detectors (BD Biosciences). Viral abundance was
determined by staining fixed seawater samples with SYBR Gold (Life
Technologies) and measurements of green fluorescence (520, 40 nm band pass).
Samples were thawed, diluted 25-fold in 0.22 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m filtered Tris/EDTA
(TE) buffer (pH 8), stained with SYBR Gold (0.5–1<inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> final
concentration), incubated for 10 min at 80 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C in the dark, cooled
to RT for 5 min, and mixed thoroughly by vortexing prior to counting on the
Influx (Brussaard, 2003). Viral abundance was analyzed using a pressure
differential (between sheath and sample fluid) of 0.7, resulting in a low
flow rate for higher event rates of virus-like particle (VLP) counts.</p>
</sec>
<sec id="Ch1.S2.SS8">
  <title>Caspase activity</title>
      <p>Biomass was collected on 25 mm, 5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m pore-size polycarbonate
filters and resuspended in 0.6–1 mL Lauber buffer (50 mM HEPES (pH 7.3),
100 mM NaCl, 10 % sucrose, 0.1 %
3-(3-cholamidopropyl)-dimethylammonio-1-propanesulfonate, and 10 mM
dithiothreitol) and sonicated on ice (four cycles of 30 s each) using an
ultra-cell disruptor (sonic dismembrator, Fisher Scientific, Waltham, MA,
USA). Cell extracts were centrifuged (10 000 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi>g</mml:mi></mml:math></inline-formula>, 2 min, room
temperature) and supernatant was collected for caspase biochemical activity.
Caspase-specific activity was determined by measuring the kinetics of
cleavage for the canonical fluorogenic caspase substrate (Z-IETD-AFC) at a
50 mM final concentration (using Ex 400 and Em 505 nm; Synergy4
BioTek, Winooski, VT, USA), as previously described in Bar-Zeev et
al. (2013). Fluorescence was converted to a normalized substrate cleavage
rate using an AFC standard (Sigma) and normalized to total protein
concentrations obtained from the same samples. Total protein concentrations
were determined by a Pierce<sup>™</sup> BCA protein assay
kit (Thermo Scientific product #23225).</p>
</sec>
<sec id="Ch1.S2.SS9">
  <title>16S rRNA gene sequencing and data analyses</title>
      <p>Bacterial community diversity was analyzed by deep sequencing of the 16S rRNA
gene in samples from two replicate bottles from experiment 1 (see Sect. 2.2)
at three time points each. Seawater samples were filtered on 25 mm,
5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m pore-size Supor filters (Pall Gelman Inc., Ann Arbor,
Michigan), snap-frozen in liquid nitrogen, and stored at <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>80 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
for later extraction. Community genomic DNA was isolated from the filters
using a phenol–chloroform extraction method modified according to Massana et
al. (1997). The 16S rRNA genes within community genomic DNA were initially
amplified with conserved bacterial primers 27F and 1100R (Dowd et al., 2008)
using a high-fidelity polymerase (Phusion DNA polymerase, Thermo Scientific)
with an initial denaturation step of 95 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for 3 min followed by 20
cycles of 95 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for 30 s, 55 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for 30 s, and
72 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for 45 s. A secondary PCR (same conditions) was performed for
next-generation sequencing by using customized fusion primers with different
tag sequences. The tags were attached to the 27F primer and to the 338R
primer (Hamady et al., 2008) to obtain 340 bp fragments suitable for
Ion Torrent analysis. Nested PCR was used to minimize inclusion of
false sequences into the sequenced material (Dowd et al., 2008). After
secondary PCR, all amplicon products were purified using Ampure magnetic
purification beads (Agencourt Bioscience Corporation, MA, USA) to exclude
primer dimers. The amplicons were sequenced at the Bar-Ilan Sequencing
Center, using an Ion Torrent<sup>™</sup> (Life
Technologies, USA).</p>
      <p>The adapter-clipped sequences were processed using tools and scripts from the
UPARSE pipeline (Edgar, 2013). Reads from all samples were pooled for
operational taxonomic unit (OTU) calling. Reads were de-multiplexed and
primers and barcodes were stripped using the script
fastq_strip_barcode_relabel.py, leaving 42 747 raw reads altogether for
six samples. As suggested for OTU calling from single-end amplicon sequences
(Edgar, 2013), sequences (mostly between 280 and 300 nt) were trimmed to a
fixed length of 280 nt, and shorter sequences were discarded (26 740
trimmed raw reads remained). For OTU clustering, trimmed raw reads were
quality-filtered using the -fastq_filter command with a maximum expected
error rate (-fastq_maxee) of 2 (21 590 reads remaining), clustered into
unicals (100 % identity) and the unicals sorted by weight (number of
sequences in the cluster). OTU clustering with an identity threshold of 0.98
was done using the -cluster_otus command on sorted unicals, with built-in
chimera filtering. To infer OTU abundances for each individual sample, the
trimmed raw reads per sample (after a more relaxed quality filtering with
-fastq_maxee 5) were mapped back to these OTUs with -usearch_global and
a minimum identity of 98 %. For taxonomic classification, OTUs were
submitted to <uri>https://www.arb-silva.de/ngs/</uri> and classified using the
SINA aligner v1.2.10 and database release SSU 123 (Quast et al., 2013).
Sequences having (BLAST alignment coverage <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> alignment
identity)/2 &lt; 93 % were considered unclassified and assigned
to the virtual group “No Relative” (5.58 % of OTUs).</p>
</sec>
<sec id="Ch1.S2.SS10">
  <title>RNA extraction and metatranscriptome sequencing</title>
      <p>Metatranscriptomic sequencing was performed for three time points: peak
surface accumulation of the bloom (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mn mathvariant="normal">0</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> 12:00), 8 h (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, 22:00), and
22 h (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, 10:00 the next day) after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. Cells on polycarbonate filters were
resuspended in 1 mL PGTX (for 100 mL final volume: phenol 39.6 g,
glycerol 6.9 mL, 8-hydroxyquinoline 0.1 g, EDTA 0.58 g, sodium
acetate 0.8 g, guanidine thiocyanate 9.5 g, guanidine hydrochloride
4.6 g, Triton X-100 2 mL) (Pinto et al., 2009) with 250 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>L
glass beads (diameter 0.1–0.25 mm). Cells were subsequently broken on a cell disruptor
(Precellys, Peqlab, Germany) at 6500 rpm for 3 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 15 s at 6500 rpm. Tubes were
placed on ice between each 15 s interval. RNA was extracted by adding
0.7 mL chloroform and subsequent phase separation. RNA was precipitated from
the aqueous phase using three volumes of isopropanol at <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>20 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
overnight. Residual DNA was removed using the Turbo DNA-free kit (Ambion)
according to the manufacturer's instructions, but adding additional 1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>l
of DNase after 30 min of incubation and incubating another 30 min. RNA was
purified using Clean &amp; Concentrator 5 columns (C&amp;C 5) (Zymo Research,
Freiburg, Germany). The pure RNA was treated with a Ribo-Zero rRNA removal kit
(Bacteria) (Epicentre, Madison, USA) and purified again with C&amp;C 5. DNA
contamination was tested and confirmed negative with a 40-cycle PCR using
cyanobacteria-specific 16S primers.</p>
      <p>For removal of tRNAs and small fragments, the RNA was purified with the
Agencourt RNAClean XP kit (Beckman Coulter Genomics, Danvers, USA).
First-strand cDNA synthesis for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> samples was primed with
a N6 randomized primer, after which the cDNAs were fragmented by ultrasound
(four pulses of 30 s at 4 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). Illumina TruSeq sequencing adapters
were ligated in a strand-specific way to the 5<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> and 3<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> ends and the
resulting cDNAs were PCR-amplified to about 10–20 ng <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
using a high-fidelity DNA polymerase. Randomly primed cDNA for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
samples was prepared using purified RNA without fragmentation followed by
ligation of Illumina TruSeq sequencing adapters to the 5<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> and 3<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> ends and
fragmentation of cDNA &gt; <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 700 bp with ultrasound (four
pulses of 30 s at 4 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C; targeting only
cDNA &gt; 700 nt). After repairing ends, fragments were dA-tailed
and Illumina TruSeq sequencing adapters were ligated again to the 5<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> and
3<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> ends of the cDNA and re-amplified. Consequently, a small fraction of the
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reads was not strand-specific. All cDNAs were purified using the
Agencourt AMPure XP kit (Beckman Coulter Genomics, Danvers, USA) and
2 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 150 nt paired-end sequences generated with an Illumina
NextSeq500 sequencer by a commercial provider (vertis AG, Freising, Germany).</p>
</sec>
<sec id="Ch1.S2.SS11">
  <title>Bioinformatics processing and analysis of metatranscriptome data</title>
      <p>To remove adapters, perform quality trimming, and set a minimal length
cutoff, raw fastq reads were processed with Cutadapt version 1.8.1 (Martin,
2011) in paired-end mode with a minimum adapter sequence overlap of 10 nt
(-O 10), an allowed error rate of 20 % (-e 0.2) in the adapter sequence
alignment, and a minimum base quality of 20. To remove residual ribosomal RNA
reads, the fastq files were further processed with SortMeRNA version 1.8
(Kopylova et al., 2012) with the accompanying standard databases in
paired-end mode, resulting in 9 469 339 non-ribosomal reads for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>,
22 407 194 for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, and 18 550 250 for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. The fastq files with
all non-ribosomal forward reads were used for mapping against the
<italic>Trichodesmium</italic> <italic>erythraeum</italic> IMS101 genome with Bowtie2
(Langmead and Salzberg, 2012) in <italic>very-sensitive-local</italic> mode. This
resulted in 51.9 % of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, 5.1 % of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, and 3.3 % of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reads mapped. Reads were counted per CDS feature as annotated in the
genome of <italic>Trichodesmium erythraeum</italic> (NC_008312.1) using htseq-count
version 0.6.0 (Anders et al., 2015) and a count table generated with all read
counts from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>For detection of differentially expressed genes from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, the count table was processed with the statistical tool
“Analysis of Sequence Counts” (ASC) (Wu et al., 2010). This tool is
specifically designed to account for missing replicates by employing a model
of biological variation of gene expression (Wu et al., 2010). The posterior
probabilities (<inline-formula><mml:math display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>) of a gene being &gt; 2-fold differentially
expressed (user-specified threshold) between any two samples is calculated
using an empirical Bayesian analysis algorithm and an internal normalization
step. Differential expression of genes was defined as significant if <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>P</mml:mi><mml:mi mathvariant="italic">&gt;</mml:mi><mml:mn> 0.98</mml:mn></mml:mrow></mml:math></inline-formula>.</p><?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
<sec id="Ch1.S3.SS1">
  <?xmltex \opttitle{Setting the scene -- \textit{Trichodesmium} bloom development and bloom within the
lagoon}?><title>Setting the scene – <italic>Trichodesmium</italic> bloom development and bloom within the
lagoon</title>
      <p><italic>Trichodesmium</italic> was present as part of the in situ community in the
lagoon at the outset of the VAHINE experiment. (Bonnet et al., 2016c;
Turk-Kubo et al., 2015). In the lagoon water, temperatures were high
(&gt; 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) and typical oligotrophic conditions of austral
summer prevailed. For the first 20 days of the experiment low abundance and
biomass was measured for primary and secondary production and specifically
for diazotrophic populations (Fig. 1). Total PON and POC in the lagoon
fluctuated in the first 20 days of the VAHINE experiment with values ranging between 0.6 and
1.1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and 5 and 11 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>,
respectively. On the morning of day 23, values were 0.9 and
9.3 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> PON and POC, respectively (Fig. 1c–d). The
total Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations ranged between 0.18 and
0.26 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> from days 1 to 19 (Fig. 1a). The increase in
Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations reflects the composite signature of the total
phototrophic community (detailed in Leblanc et al., 2016; Van Wambeke et al.,
2015) and is not specific to <italic>Trichodesmium</italic> biomass. Low abundances
of <italic>Trichodesmium</italic> were measured in the lagoon waters throughout the
first 3 weeks of the project (Turk-Kubo et al., 2015), with
<italic>Trichodesmium</italic>-associated 16S tags ranging from 0.1 to 0.4 % of
the total number of 16S tags (Pfreundt et al., 2016). During the first
eight days of sampling, <italic>Trichodesmium</italic> abundance, as measured by
<italic>nifH</italic> gene real-time PCR, ranged from
3.4 <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">2</mml:mn></mml:msup></mml:math></inline-formula>–6.5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> <italic>nifH</italic>
copies L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. By days 14 and 16, <italic>Trichodesmium</italic> accounted for
15 % of the total diazotroph population (with
1.1–1.5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msup></mml:math></inline-formula> <italic>nifH</italic> copies L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, increasing by
day 22 to 42 % of the diazotroph population (1.4 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula>
<italic>nifH </italic>copies L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Turk-Kubo et al., 2015). By the morning of
day 23, Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> increased to 0.39 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the upper 1 m
depth (Fig. 1a), yet <italic>Trichodesmium</italic> was still not visually observed
at this time as a bloom on the sea surface. Phycoerythrin concentrations
fluctuated between 0.1 and 0.4 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> during days 1–14 and
then increased to a maximal peak of &gt; 0.8 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
on day 21 with values <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>on day 23, reflecting
both the doubling in <italic>Synechococcus</italic> biomass (days 15–23) and
increasing <italic>Trichodesmium</italic> (days 21–23) (Leblanc et al., 2016).
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rates in the lagoon waters ranged between
0.09–1.2 nmol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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> during the pre-bloom period (Fig. 1c)
and on the morning of day 23 were measured at
0.5 nmol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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> (Fig. 1c).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>Temporal dynamics of pre-bloom measurements in the lagoon
waters. <bold>(a)</bold> Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <bold>(b)</bold>
Virus-like particles (VLP, mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, <bold>(c)</bold>
N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rates (nmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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 particulate organic
nitrogen (PON, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <bold>(d)</bold> Changes in the
concentrations of transparent exopolymeric particles (TEP, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and particulate organic carbon (POC, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>.
Water was sampled from the lagoon outside the VAHINE mesocosms, at 1 m
depth (surface) throughout the experimental period from day 2 to 23 (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula>).
For VLP, the standard error for technical replicates (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula>) was
&lt; 1 %, which is smaller than symbol size.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f01.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><caption><p><bold>(a–c)</bold> Dense surface blooms of <italic>Trichodesmium</italic>
observed outside the mesocosms in the lagoon waters on day 23 at 12:00 LT.
Photos illustrate the spatial heterogeneity of the surface accumulations and
the high density of the biomass. <bold>(d–e)</bold> To examine the mechanistic
of demise (experiment 1), <italic> Trichodesmium</italic> filaments and colonies were
collected with a plankton net (mesh size, 80 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m) from the dense
surface bloom (day 23, 12:00 LT; designated <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and resuspended in
0.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m pore-size filtered seawater (FSW) in six 4.5 L bottles.
Bottles were incubated on-deck in running-seawater pools with ambient surface
temperature (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 26 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) at 50 % of the surface irradiance.
Bottles were sampled every 2–4 h for different parameters until the biomass
crashed. <bold>(f)</bold> Temporal changes in Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations in the
bottles from the time of biomass collection and resuspension in the bottles
until the <italic>Trichodesmium</italic> biomass crashed <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 24 h after the
experiment began (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula>–6). Photo c. courtesy of A. Renaud.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f02.jpg"/>

        </fig>

      <p>Zooplankton populations in the lagoon fluctuated around 5000
individuals m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and increased from day 9 to 16, peaking at
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 14 000 individuals m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Hunt et al., 2016). From day 16 to 23
the total zooplankton population declined to <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 8000
individuals m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> with harpacticoid copepods, including grazers of
<italic>Trichodesmium</italic> (<italic>Macrosetella gracilis</italic>, <italic>Miracia efferata</italic>, and <italic>Oculosetella gracilis</italic>), comprising
&lt; 1.5 % of total zooplankton community in the lagoon (Hunt et
al., 2016). VLP typically ranged from 1–6 <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> mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
throughout the first 22 days of the VAHINE experiment and displayed a
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2–4-day oscillation (i.e., increasing for 2 days, then declining for
the next 3 days, etc.) with mean values of 3.8 <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:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(Fig. 1b). VLP counts in surface waters on day 23 were
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:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 1b), just prior to the appearance of
the <italic>Trichodesmium</italic> surface bloom. VLP did not show any distinct
correlations with total biomass indices such as PON and POC during the
pre-bloom sampling (Fig. 1b–d).</p>
      <p>Depth-averaged dissolved inorganic phosphorus (DIP) concentrations in the
lagoon waters were low, at 0.039 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.001 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>M, with a
relatively stable DIP turnover time (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mtext>DIP</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> of 1.8 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.7 days
for the first 15 days, which declined to 0.5 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.7 by day 23 (Berthelot
et al., 2015). Alkaline phosphatase activity (APA), which hydrolyzes
inorganic phosphate from organic phosphorus, increased <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 3-fold, from
1.8 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.7 (average of days 1–4) to
5.0 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 1.4 nmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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> (average of days 19–23) (Van
Wambeke et al., 2015), demonstrating a response in metabolic activity related
to P acquisition for the microbial community probably related to the
decreasing availability of DIP in the lagoon waters.</p>
      <p>On day 23 (4 February) of the VAHINE measurements, dense surface
accumulations of <italic>Trichodesmium</italic> were observed at midday
(12:00) (Fig. 2a–c). Ambient
air temperatures (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) increased to over 26 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
and the winds decreased to &lt; 5 kn. These accumulations (hereafter
blooms) appeared in the typical “slick” formations of dense biomass in
ribbons visible on the surface seawater and spread out over tens of meters in
the lagoon water outside the mesocosms (Fig. 2a–c). <italic>Trichodesmium</italic>
abundance in these patches was extremely variable, with Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>
concentrations exceeding 5 mg L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> within dense patches and trichome
abundance &gt; 10 000 trichomes L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. These surface
accumulations were visible and sampled again 5 h later (experiment 2), yet
by the next morning, no such slicks or patches of dense biomass were observed
or measured in the lagoon. The disappearance of the <italic>Trichodesmium</italic> in
the lagoon water, whether by drifting away, sinking to depth, or any other
factor, prevented further investigation of these populations.</p>
</sec>
<sec id="Ch1.S3.SS2">
  <?xmltex \opttitle{Investigating \textit{Trichodesmium} mortality in experimental
microcosms}?><title>Investigating <italic>Trichodesmium</italic> mortality in experimental
microcosms</title>
<sec id="Ch1.S3.SS2.SSS1">
  <?xmltex \opttitle{Changes in \textit{Trichodesmium} biomass and associated microbial
communities}?><title>Changes in <italic>Trichodesmium</italic> biomass and associated microbial
communities</title>
      <p>The spatially patchy nature of <italic>Trichodesmium</italic> blooms in the lagoon
(Fig. 2a–c), and the rapid temporal modifications in water-column abundance
of filaments and colonies probably induced by physical drivers
(turbulence and wind-stress), complicate in situ sampling when
targeting changes in specific biomass. To overcome this, we collected
<italic>Trichodesmium</italic> populations from the surface midday bloom and examined
the physiological, biochemical, and gene expression changes occurring with time until
the biomass crashed after <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 24 h (see methods Sect. 2.2) (Figs. 2 and 3). In
these enclosed microcosms, <italic>Trichodesmium</italic> 16S copies comprised
&gt; 90 % of total copies (Fig. 3), enabling the use of Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> to
follow changes in its biomass (Fig. 2f). Maximal Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations in
the incubations (&gt; 150 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 80 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>; <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">6</mml:mn></mml:mrow></mml:math></inline-formula>)
were measured at the start of the incubation soon after the biomass
collection and resuspension in FSW. These<italic> Trichodesmium</italic> populations
collapsed swiftly over the next day, with Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentrations declining to
24 and 11 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> after 10 and 22 h, respectively
(Fig. 2f).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>Dynamics of microbial community abundance and diversity during
<italic>Trichodesmium</italic> surface bloom as obtained by 16S rRNA gene sequencing
for samples collected from the surface waters outside the mesocosms during
<italic>Trichodesmium</italic> surface accumulation (bloom) (short-term
experiment 1). Pie charts show the changes in dominant groups during the bloom and crash from two replicate incubation bottles
(note that Oscillatoriales consisted only of
<italic>Trichodesmium</italic> in this experiment). The graphs below show the
respective temporal dynamics of <italic>Trichodesmium</italic> (gray circles) and
<italic>Alteromonas</italic> (white triangles), the dominant bacterial species during
the incubation experiment.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f03.png"/>

          </fig>

      <p>In experiment 1 we characterized the microbial community associated with the
<italic>Trichodesmium</italic> biomass within the microcosms by 16S rRNA gene
sequencing from two replicate bottles (experiment 1). At <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> 94 and
93 % of the obtained 16S tags in both replicates (Fig. 3) were of the
Oscillatoriales order (phylum Cyanobacteria), with 99.9 % of these
sequences classified as <italic>Trichodesmium</italic> spp. (Fig. 3). In both
replicates, the temporal decline of <italic>Trichodesmium</italic> biomass coincided
with an increase in <italic>Alteromonas</italic> 16S tags, but this development
temporally lagged in replicate 1 compared to replicate 2 (Fig. 3). Six hours
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">6</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> after the surface bloom was originally sampled (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, over
80 % of the 16S tags from replicate 1 were characterized as
<italic>Trichodesmium</italic>. Fourteen hours after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, Alteromonadales and Vibrionales
replaced <italic>Trichodesmium</italic>, thereafter constituting only 9 % of 16S tags
(Fig. 3). In replicate 2, <italic>Trichodesmium</italic> declined by 80 % 6 h
after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, with Alteromonadales and Flavobacteriales comprising the bulk
of the biomass 18 h after the start of incubations (Fig. 3).</p>
      <p>The rate of decline in <italic>Trichodesmium</italic> biomass within the 4.6 L
microcosms paralleled that of <italic>Trichodesmium</italic> collected from the
surface accumulations at 17:00 and incubated in 20 L carboys under ambient
conditions for &gt; 72 h (defined hereafter as experiment 2:
Fig. 4). Here, <italic>Trichodesmium</italic> biomass decreased by
&gt; 80 % within 24 h of incubations with trichome abundance
declining from <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 2500 trichomes L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> at bloom collection to
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 495 trichomes L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 4a). No direct correlation was
observed between the decline of <italic>Trichodesmium</italic> and viral populations.
VLP abundance at the time of the surface bloom sampling was at a maximum of
8.2 <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> mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 4a), decreasing to
5.7 <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> mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> in the next 4 h and then remaining stable
throughout the crash period (within the next 42 h), averaging
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 5 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.7 mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 4a).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Short-term experiment 2 –  measurements from the lagoon waters
following <italic>Trichodesmium</italic> bloom on day 23. <bold>(a)</bold> <italic>Trichodesmium</italic>
abundance (trichomes L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> derived from qPCR-based abundances of
<italic>Trichodesmium</italic> <italic>nifH</italic> gene copies (Bonnet et al., 2016b) based
on the assumption of 100 gene copies per trichome and virus-like
particles (VLP, mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <bold>(b)</bold> N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rates (nmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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>, particulate organic nitrogen (PON,
<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, and ammonium concentrations (NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>,
nmol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <bold>(c)</bold> Changes in the concentrations of
transparent exopolymeric particles (TEP, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and
particulate organic carbon (POC, <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. For experiment 2,
seawater from the surface bloom was collected 5 h after the initial surface
bloom was sighted (day 23, 17:00 LT) by
directly filling 20 L polyethylene carboys gently to avoid destroying
biomass. Bottles were placed in on-deck incubators filled with running
seawater to maintain ambient surface temperature (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 26 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) and
covered with neutral screening at 50 % surface irradiance levels. For all
parameters, replicates were <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula>. For VLP, the standard error for technical
replicates (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula>) was &lt; 1 %, which is smaller than symbol
size.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f04.png"/>

          </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p><bold>(a)</bold> Expression of alkaline phosphatase associated genes
<italic>phoA</italic> and <italic>phoX</italic> (Tery_3467 and Tery_3845); phosphite utilization genes
<italic>ptxA</italic>, <italic>ptxB</italic>, and <italic>ptxC</italic> (Tery_0365, Tery_0366, and Tery_0367); and
phosphonate utilization genes (<italic>phn </italic> genes, Tery_4993, Tery_4994,
Tery_4995, Tery_4996<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula>, Tery_4997, Tery_4998, Tery_4999, Tery_5000,
Tery_5001 Tery_5002 and Tery_5003). Asterisks near locus tag numbers
indicate gene duplicates. <bold>(b)</bold> Iron-related genes, <italic>isiB</italic>
(Tery_1666), <italic>isiA</italic> (Tery_1667), <italic>idiA</italic> (Tery_3377), and ferritin DPS gene
<italic>dpsA</italic> (Tery_4282). Bars represent log2-fold changes of corresponding genes
at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (8 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (22 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> in
comparison to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. A significant change in expression from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> was tested with ASC (Wu et al.,
2010) and marked with an asterisk. A gene was considered differentially expressed if <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>P</mml:mi><mml:mi mathvariant="italic">&gt;</mml:mi><mml:mn> 0.98</mml:mn></mml:mrow></mml:math></inline-formula> (posterior probability).</p></caption>
            <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f05.png"/>

          </fig>

      <p>As <italic>Trichodesmium</italic> crashed in the experimental incubations, high
values of NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> were measured (Fig. 4b). In experiment 2, NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>
increased exponentially from 73 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.4 nmol NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> when
the surface bloom was collected and placed in the carboys (17:00) to
1490 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 686 after 24 h and values &gt; 5000 nmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
42 h after the incubation start (Fig. 4b). The high ammonia declined
somewhat by the end of the experiment (after 72 h), yet was still high at
3494 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 834 nmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Concurrently with the high NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>
concentrations, and despite the dying <italic>Trichodesmium,</italic> we measured an
increase N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation rates. N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fixation rose from 1.5 at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to
3.5 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 2.8 nmol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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> 8 h after incubations began and
11.7 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 3.4 nmol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> h<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> 24 h later (Fig. 4b). These
high values represent other diazotrophs including UCYN types and
diatom–diazotroph associations that flourished after the
<italic>Trichodesmium</italic> biomass had declined in the carboys (Bonnet et al.,
2016b; K. Turk-Kubo, personal communication, 2016). POC and PON, representing
the fraction of C and N incorporated into biomass, ranged between 5.2 and
11.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol C L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and 0.6 and 1.1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
during pre-bloom periods (Fig. 1c–d) and
12.6 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 4.6 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol C L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
1.3 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> when the surface bloom was sampled
(Fig. 4b–c). Twenty-four hours after collection of bloom biomass, POC
increased <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 6-fold to 63.2 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 15 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol C L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and
PON increased 10-fold to 10 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 3.3 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(Fig. 4b–c). After 72 h, total POC was 62 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 4 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol
C L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 4c) and PON increased to 14.1 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 6 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol
N L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 4b).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p><bold>(a)</bold> Dynamics of caspase-specific activity rates
(pmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> mg protein<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> min<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>) of <italic>Trichodesmium</italic> in
the New Caledonian lagoon during bloom accumulation and bloom demise, sampled
during experiment 1. Samples (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">6</mml:mn></mml:mrow></mml:math></inline-formula>) collected from the bloom (day 23,
12:00 LT, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> were incubated on-deck in an incubator fitted with
running seawater to maintain ambient surface temperature (see Methods).
<bold>(b)</bold> Transcript accumulation of metacaspase genes in the
<italic>Trichodesmium</italic> bloom during the short-term incubation experiment.
Metacaspase genes are TeMC1 (Tery_2077), TeMC2 (Tery_2689), TeMC3
(Tery_3869), TeMC4 (Tery_2471), TeMC5 (Tery_2760), TeMC6
(Tery_2058), TeMC7 (Tery_1841), TeMC8 (Tery_0382), TeMC9
(Tery_4625), TeMC10 (Tery_2624), and TeMC11 (Tery_2158). Bars
represent log2-fold changes at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (8 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
(22 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> in comparison to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. Significant change in
expression from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> was tested with ASC (Wu et al., 2010) and marked with
an asterisk. A gene was considered differentially expressed if <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>P</mml:mi><mml:mi mathvariant="italic">&gt;</mml:mi><mml:mn> 0.98</mml:mn></mml:mrow></mml:math></inline-formula> (posterior probability).</p></caption>
            <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f06.png"/>

          </fig>

      <p>Organic carbon in the form of TEP is secreted when <italic>Trichodesmium</italic> is
stressed and undergoing PCD (Bar-Zeev et al., 2013; Berman-Frank et al.,
2004). TEP concentrations in the lagoon waters during the pre-bloom period
(first 20 days) fluctuated around <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 350 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 1d) that increased to <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 500 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> on day 22 (Fig. 1d). During the time of biomass collection from
the surface bloom TEP concentration exceeded 700 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn> 1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(Fig. 4c). After biomass enclosure (experiment 2) TEP concentrations declined
to 420 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 35 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and subsequently to
180 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 25 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> 42 h and 72 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
(Fig. 4c).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><caption><p>Change in gas vesicle protein (<italic>gvp</italic>) genes as obtained from
metatranscriptomic analyses of the <italic>Trichodesmium</italic> bloom from peak to
collapse (experiment 1). <italic>gvpA</italic> genes (Tery_2330 and Tery_2335<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula>)
encode the main constituent of the gas vesicles that forms the essential core
of the structure; <italic>gvpN</italic> (Tery_2329 and Tery_2334<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula>), <italic>gvpK</italic>
(Tery_2322), <italic>gvpG</italic> (Tery_2338), and <italic>gvpL/gvpF</italic> (Tery_2339
and Tery_2340<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>*</mml:mo></mml:msup></mml:math></inline-formula>) encode vesicle synthesis proteins. Asterisks near locus tag numbers indicate
gene duplicates. Bars represent log2-fold changes at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (8 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (22 h
after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> in comparison to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. Significant change in expression from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> was tested with ASC
(Wu et al., 2010) and marked with an asterisk. A gene was considered differentially expressed
if <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>P</mml:mi><mml:mi mathvariant="italic">&gt;</mml:mi><mml:mn>0.98</mml:mn></mml:mrow></mml:math></inline-formula> (posterior probability).</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/4187/2016/bg-13-4187-2016-f07.png"/>

          </fig>

</sec>
<sec id="Ch1.S3.SS2.SSS2">
  <?xmltex \opttitle{Genetic responses of stressed \textit{Trichodesmium}}?><title>Genetic responses of stressed <italic>Trichodesmium</italic></title>
      <p>Metatranscriptomic analyses of the <italic>Trichodesmium</italic> biomass were
conducted in samples from experiment 1, at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
(Fig. S1). We examined differential expression during this period by
investigating a manually curated gene suite including specific pathways
involved in P and Fe uptake and assimilation, PCD, or gas vesicle synthesis.
Genes involved in the acquisition and transport of inorganic and organic P
sources were upregulated, concomitant with biomass demise; significantly
higher expression levels were evident at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> compared to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Table S1). Abundance of alkaline phosphatase transcripts, encoded by
the <italic>phoA</italic> gene (Orchard et al., 2003), increased significantly
(<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 5-fold) from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5a). The transcript abundance
of phosphonate transporters and C-P lyase genes (<italic>phnC</italic>, <italic>phnE</italic>, <italic>phnH</italic>,
<italic>phnI</italic>, <italic>phnL</italic>, and <italic>phnM</italic>)
increased significantly (5–12-fold) between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5a, Table S1). Of the phosphite uptake genes, only <italic>ptxA</italic>
involved in the phosphite (reduced inorganic phosphorus compound) uptake
system, and recently found to operate in <italic>Trichodesmium</italic>
(Martínez et al., 2012; Polyviou et al., 2015), was significantly
upregulated at both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> compared to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (4.5- and 7-fold
change, respectively). The two additional genes involved in phosphite uptake,
<italic>ptxB</italic> and <italic>ptxC</italic>, did not change significantly, as
<italic>Trichodesmium</italic> biomass crashed (Fig. 5a).</p>
      <p>As Fe limitation induces PCD in <italic>Trichodesmium</italic> (Berman-Frank et al.,
2004, 2007), we examined genetic markers of Fe
stress. At the time of surface bloom sampling (experiment 1, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, Fe
stress was indicated by higher differential expression of several genes. The
<italic>isiB</italic> gene encodes flavodoxin and serves as a common diagnostic indicator of
Fe stress in <italic>Trichodesmium</italic>, since it may substitute for Fe–S-containing ferredoxin (Bar-Zeev et al., 2013; Chappell and Webb, 2010).
Transcripts of <italic>isiB</italic> were significantly higher at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (3-fold) than at
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5b, Table S1). The chlorophyll-binding protein
IsiA is induced in cyanobacterial species under Fe or oxidative stress to
prevent oxidative damage (Laudenbach and Straus, 1988). Here <italic>isiA</italic>
transcripts increased 2- and 3-fold from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>,
respectively (Fig. 5b, Table S1). The Fe transporter gene <italic>idiA</italic> showed a
transient higher transcript accumulation only at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. As the health of
<italic>Trichodesmium</italic> declined, transcripts of the Fe-storage protein
ferritin (Dps) decreased by &gt; 70 % at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5b,
Table S1)</p>
</sec>
<sec id="Ch1.S3.SS2.SSS3">
  <title>PCD-induced demise</title>
      <p>Our earlier work demonstrating PCD in <italic>Trichodesmium</italic> allowed us to
utilize two independent biomarkers to investigate PCD induction during
<italic>Trichodesmium</italic> demise, namely changes in catalytic rates of
caspase-specific activity (Berman-Frank et al., 2004, 2007) and levels of
metacaspase transcript expression (Bar-Zeev et al., 2013). When the surface
bloom was sampled (experiment 1, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, protein normalized
caspase-specific activity was very low at
0.23 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.2 pmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> mg protein<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> min<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> (Fig. 6a).
After a slight decline in the first 2 h, caspase activity increased
throughout the experiment with 10-fold higher values
(2.9 <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 1.5 pmol L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> mg protein<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> min<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> obtained
over the next 22 h as the bloom crashed (Fig. 6a).</p>
      <p>We followed transcript abundance over the demise period for the 12 identified
metacaspase genes in <italic>Trichodesmium</italic> (Asplund-Samuelsson et al., 2012;
Asplund-Samuelsson, 2015; Berman-Frank et al., 2004): TeMC1 (Tery_2077),
TeMC2 (Tery_2689), TeMC3 (Tery_3869), TeMC4 (Tery_2471), TeMC5
(Tery_2760), TeMC6 (Tery_2058), TeMC7 (Tery_1841), TeMC8
(Tery_0382), TeMC9 (Tery_4625), TeMC10 (Tery_2624), TeMC11
(Tery_2158), and TeMC12 (Tery_2963) (Fig. 6b, Table S1). A subset of
these genes was previously shown to be involved in PCD of <italic>Trichodesmium</italic>
cultures in response to Fe and light stress (Bar-Zeev et al., 2013, 2004;
Bidle, 2015). Here, we interrogated the entire suite of metacaspases in
natural <italic>Trichodesmium</italic> populations. As the biomass crashed from
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, 7 out of 12 metacaspases (TeMC1, TeMC3, TeMC4, TeMC7,
TeMC8, TeMC9, and TeMC11) were significantly upregulated 8 and 22 h after
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 6b). For these genes, transcript abundance increased 2.3- to
5.3-fold 8 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and 3.5–6.2-fold 22 h after <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 6b,
Table S1) TeMC5 and TeMC10 transcripts increased significantly after 22 h by
2.9- and 3.2-fold, respectively. TeMC6 was upregulated 2.9-fold after 8 h.
TeMC2 transcripts did not significantly change over time. We did not detect
any expression of TeMC12 throughout the experiment.</p>
      <p>Export flux can be enhanced by PCD-induced sinking (Bar-Zeev et al., 2013) as
PCD in <italic>Trichodesmium</italic> results in degradation of internal components,
especially gas vesicles that are required for buoyancy (Berman-Frank et al.,
2004). Although we did not measure changes in buoyancy itself, we observed
rapid sinking of the <italic>Trichodesmium</italic> biomass in the bottles and
carboys. The metatranscriptomic analyses demonstrated that, excluding one
copy of <italic>gvpL/gvpF</italic>, gas vesicle
protein <italic>(gvp)</italic> genes involved in gas vesicle formation (<italic>gvpA</italic>, <italic>gvpN</italic>, <italic>gvpK</italic>,
<italic>gvpG</italic>, and <italic>gvpL/gcpF</italic>) were all significantly downregulated relative to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
(Fig. 7, Table S1).</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <?xmltex \opttitle{Mortality processes of \textit{Trichodesmium} -- incubation
results}?><title>Mortality processes of <italic>Trichodesmium</italic> – incubation
results</title>
<sec id="Ch1.S4.SS1.SSS1">
  <title>Grazer and virus influence</title>
      <p>Our microcosm incubations allowed us to specifically focus on the loss
factors and show the involvement of biotic and abiotic stressors in inducing
PCD and mechanistically impacting the demise and fate of a natural
<italic>Trichodesmium</italic> bloom. We recognize that the enclosure and incubation of collected biomass
in bottles and carboys may accelerate cellular processes compared to the natural
lagoon setting. However, the published rates of <italic>Trichodesmium</italic> mortality
from field studies (Rodier and Le Borgne, 2010) indicate that these can
parallel our loss rates with natural bloom demise occurring 24–48 h after
peak of biomass.</p>
      <p>We focused initially on biotic factors that could impact the incubated
<italic>Trichodesmium</italic> biomass. The low number of harpacticoid zooplankton
specific to <italic>Trichodesmium</italic> (O'Neil and Roman, 1994; O'Neil, 1998) in
the lagoon (Hunt et al., 2016) and especially those in the bottles (personal
observation) refutes the possibility that grazing caused the massive mortality
of <italic>Trichodesmium</italic> biomass in our experimental incubations.</p>
      <p>Viruses have been increasingly invoked as key agents terminating
phytoplankton blooms (Brussaard et al., 2005; Jacquet et al., 2002; Lehahn et
al., 2014; Tarutani et al., 2000; Vardi et al., 2012). Infection by phages
has been invoked as the mechanism of <italic>Trichodesmium</italic> bloom crashes,
but it has yet to be unequivocally demonstrated (Hewson et al., 2004; Ohki,
1999); indeed, no specific <italic>Trichodesmium</italic> phage has been isolated or
characterized to date (Brown et al., 2013). Here, total VLP abundance was
highest at the time of sampling from the surface <italic>Trichodesmium</italic> bloom
and at the start of the incubation (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 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:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula>
VLP mL<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). It actually declined 2-fold in the first 8 h of incubation
before increasing over the next 32 h (Fig. 4a). While our method of analysis
cannot distinguish between phages infecting <italic>Trichodesmium</italic> from those
infecting other marine bacteria, it argues against a massive, phage-induced
lytic event of <italic>Trichodesmium</italic>. Such an event would have yielded a
notable burst of VLP upon bloom crash, especially considering the high
<italic>Trichodesmium</italic> biomass observed. The coincidence between the maximal
abundance of VLP and highest <italic>Trichodesmium</italic> biomass is counter to
viruses serving as the mechanism of mortality in our incubation experiments.
Nonetheless, virus infection itself may be a stimulant for community N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fixation perhaps by releasing key nutrients (i.e., P or Fe) upon lysis of
surrounding microbes (Weitz and Wilhelm, 2012). Although we did not
characterize them here, it is indeed possible that
<italic>Trichodesmium</italic>-specific phages were present in our incubation
experiments and they may have exerted additional physiological stress on
resident populations, facilitating PCD induction. Virus infection has been
shown to increase the cellular production of reactive oxygen species (Evans
et al., 2006; Vardi et al., 2012), which in turn can stimulate PCD in algal
cells (Berman-Frank et al., 2004; Bidle, 2015; Thamatrakoln et al., 2012).
Viral attack can also directly trigger PCD as part of an antiviral defense
system activated to limit virus production and prevent massive viral
infection (Bidle and Falkowski, 2004; Bidle, 2015; Georgiou et al., 1998).</p>
</sec>
<sec id="Ch1.S4.SS1.SSS2">
  <title>Stressors impacting mortality</title>
      <p>Nutrient stress can be acute or chronic to which organisms may acclimate on
different timescales. Thus, for example, the consistently low DIP
concentrations measured in the lagoon during the 22 days preceding the
<italic>Trichodesmium</italic> surface bloom probably enabled acclimation responses
such as induction of APA and other P acquisition systems.
<italic>Trichodesmium</italic> has the ability to obtain P via inorganic and organic
sources, including methylphosphonate, ethylphosphonate, and
2-aminoethylphosphonate (Beversdorf et al., 2010; Dyhrman et al., 2006), and via a phosphite uptake system (PtxABC) that accesses P via the reduced
inorganic compound phosphite (Martínez et al., 2012; Polyviou et al.,
2015). Our metatranscriptomic data demonstrated upregulated expression of
genes related to all three of these uptake systems (DIP, phosphonates,
phosphites) 8 and 22 h after incubation began, accompanying biomass demise
(Fig. 5a). This included one gene for phosphite uptake (<italic>ptxA</italic>) and several
genes from the phosphonate uptake operon (<italic>phn</italic>DCEEGHIJKLM) (Hove-Jensen et
al., 2014). Upregulated expression of <italic>phnD</italic>, <italic>phnC</italic>, <italic>phnE</italic>, <italic>phnH</italic>, <italic>phnI</italic>, <italic>phnJ</italic>,
<italic>phnK</italic>, <italic>phnL</italic>, and <italic>phnM</italic> occurred as the <italic>Trichodesmium</italic> biomass
crashed (Fig. 5a, Table S1), consistent with previous results demonstrating
that <italic>phnD</italic> and <italic>phnJ</italic> expression levels increased during DIP depletion
(Hove-Jensen et al., 2014). It is likely that, during bloom demise, the C-P
lyase pathway of remaining living cells was induced when DIP sources were
extremely low, while POP and DOP increased along with the decaying organic
matter. The ability to use phosphonates or phosphites as a P source can
provide a competitive advantage for phytoplankton and bacteria in P-depleted
waters (Coleman and Chisholm, 2010; Martinez et al., 2010). Thus, it is
puzzling why dying cells would upregulate <italic>phn</italic> genes or <italic>phoA</italic> transcripts
after 22 h incubation (Fig. 5a). A more detailed temporal resolution of the
metatranscriptomic analyses may elucidate the expression dynamics of these
genes and their regulating factors. Alternatively, in PCD-induced
populations, a small percentage of cells remain viable and resistant as either cysts
(Vardi et al., 1999) or hormogonia (Berman-Frank et al., 2004) that can serve
as the inoculum for future blooms. It is plausible that the observed
upregulation signal was attributable to these subpopulations.</p>
      <p>The concentrations of dissolved and bioavailable Fe were not measured in the
lagoon water during the experimental period as Fe is typically replete in the
lagoon (Jacquet et al., 2006). However, even in Fe-replete environments such
as the New Caledonian lagoon, dense patches of cyanobacterial or algal
biomass can deplete available resources and cause limited microenvironments
(Shaked, 2002). We obtained evidence for Fe stress using several proxy genes
demonstrating that enhanced cellular Fe demand occurred during the bloom
crash (Table S1). <italic>Trichodesmium</italic>'s strategies of obtaining and
maintaining sufficient Fe involves genes such as <italic>isiB</italic>. <italic>isiB</italic>
was highly expressed when biomass accumulated on the surface waters,
indicative for higher Fe demand at this biomass load (Bar-Zeev et al., 2013;
Chappell and Webb, 2010), yet expression declined significantly with the
dying biomass. Transcripts for chlorophyll-binding, Fe-stress-induced protein
A (IsiA) increased (albeit not significantly) 3-fold over 22 h of bloom
demise (Fig. 5b, Table S1). In many cyanobacteria, <italic>isiA</italic> expression
is stimulated under Fe stress (Laudenbach and Straus, 1988) and oxidative
stress (Jeanjean et al., 2003) and functions to prevent high light-induced
oxidative damage by increasing cyclic electron flow around the photosynthetic
reaction center photosystem I (Havaux et al., 2005; Latifi et al., 2005;
Michel and Pistorius, 2004). Dense surface blooms of <italic>Trichodesmium</italic>
are exposed to high irradiance (on day 23 average photosynthetically active
radiation was 3000 <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>. It is
possible that high Fe demand combined with the oxidative stress of the high
irradiance induced the higher expression of <italic>isiA</italic> (Fig. 5b). As cell
density and associated self-shading of <italic>Trichodesmium</italic> filaments
decreased during bloom crash, light-induced oxidative stress is likely the
principal driver for elevated <italic>isiA</italic> expression.</p>
      <p>The gene <italic>idiA</italic> is another environmental Fe stress biomarker that allows
acquisition and transfer of Fe through the periplasm into the cytoplasm
(Chappell and Webb, 2010). In our incubation, upregulated expression of
<italic>idiA</italic> (an ABC Fe<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> transporter) was evident after 8 h. This is
consistent with increasing Fe limitation, as <italic>Trichodesmium</italic> abundance
(measured via 16S rRNA gene sequencing) was still high at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">6</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (after 6 h
of incubation) (replicate 1). These findings are consistent with proteomics
analyses from depleted iron (0 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>M Fe) <italic>Trichodesmium</italic>
cultures which revealed an increase in IdiA protein expression (Snow et al.,
2015). Lastly, our metatranscriptomic data highlighted a reduction in Fe
storage and utilization, as the expression of Fe-rich ferritin-like DPS
proteins (Castruita et al., 2006), encoded by <italic>dpsA</italic>, decreased <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 5-fold by the time that most of the biomass had crashed (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Fig. 5b,
Table S1). <italic>dpsA</italic> was also downregulated under Fe-replete conditions in
<italic>Synechococcus</italic> (Mackey et al., 2015), but the downregulation observed
here is more likely related to <italic>Trichodesmium</italic> cells dying and
downregulating Fe-demanding processes such as photosynthesis and N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fixation.</p>
</sec>
<sec id="Ch1.S4.SS1.SSS3">
  <title>Programmed cell death (PCD) and markers for increased export
flux</title>
      <p>The physiological and morphological evidence of PCD in <italic>Trichodesmium</italic>
has been previously documented in both laboratory (Bar-Zeev et al., 2013;
Berman-Frank et al., 2004) and environmental cultures collected from surface
waters around New Caledonia (Berman-Frank et al., 2004). Here, we confirmed
characteristic features of autocatalytic PCD in <italic>Trichodesmium</italic> such
as increased caspase-specific activity (Fig. 6a), globally enhanced
metacaspase expression (Fig. 6b), and decreased expression of gas vesicle
maintenance (Fig. 7). Metatranscriptomic snapshots interrogating expression
changes in all of the annotated <italic>Trichodesmium</italic> metacaspases (Fig. 6b)
generally portrayed upregulated expression concomitant with biomass decline.
Our results are consistent with previous observations that Fe-depleted
PCD-induced laboratory cultures of <italic>Trichodesmium</italic> IMS101 had higher
expression levels of TeMC1 and TeMC9 compared to healthy Fe-replete
cultures (Bar-Zeev et al., 2013; Berman-Frank et al., 2004). To our
knowledge, this is the first study examining expression levels of
metacaspases in environmental <italic>Trichodesmium</italic> samples during a natural
bloom. Eleven of the 12 metacaspases in <italic>Trichodesmium</italic> were expressed
in all three metatranscriptomes from the surface bloom. To date, no specific
function has been determined for these metacaspases in <italic>Trichodesmium</italic>
other than their association with cellular stress and death. Efforts are
underway to elucidate the specific cellular functions, regulation, and
protein interactions of these <italic>Trichodesmium</italic> metacaspases (Bar-Zeev
et al., 2013; Pfreundt et al., 2014; D. Spungin, personal communication,
2016).</p>
      <p>In cultures and isolated natural populations of <italic>Trichodesmium</italic>, high
caspase-like specific activity is correlated with the initial induction
stages of PCD with activity declining as the biomass crashes (Bar-Zeev et
al., 2013; Berman-Frank et al., 2004, 2007). Here, caspase-like activity
increased with the crashing populations of <italic>Trichodesmium</italic> (Fig. 6a).
Notably, maximal caspase activities were recorded at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, after which
most <italic>Trichodesmium</italic> biomass had collapsed. The high
protein-normalized caspase-specific activity may be a result of a very
stressed and dying subpopulation of <italic>Trichodesmium</italic> that had not yet
succumbed to PCD (Berman-Frank et al., 2004). Alternatively, the high
caspase-like activity may be attributed to the large population of
<italic>Alteromonas</italic> bacteria that were associated with the remaining
detrital <italic>Trichodesmium</italic> biomass. However, currently, we are unaware
of any publications demonstrating high cellular caspase-specific activity in
clades of <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">γ</mml:mi></mml:math></inline-formula>-Proteobacteria.</p>
      <p>Gas vesicles are internal structures essential for maintaining buoyancy of
<italic>Trichodesmium</italic> populations in the upper surface waters enabling them
to vertically migrate and respond to light and nutrient requirements (Capone
et al., 1997; Walsby, 1978). Mortality via PCD causes a decline in the number
and size of cellular gas vesicles in <italic>Trichodesmium</italic> (Berman-Frank et
al., 2004) and results in an enhanced vertical flux of trichomes and colonies
to depth (Bar-Zeev et al., 2013). Our metatranscriptomic data supported the
subcellular divestment from gas vesicle production during bloom decline, as
the expression of vesicle-related genes was downregulated (Fig. 7). In
parallel, TEP production and concentration increased to
&gt; 800 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g GX L<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, a 2-fold increase from pre-bloom
periods (Figs. 1d and 4c). When nutrient uptake is limited, but CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and
light are sufficient, uncoupling occurs between photosynthesis and growth
(Berman-Frank and Dubinsky, 1999), leading to increased production of excess
polysaccharides (such as TEP) and corresponding with high TEP found in bloom
decline phases rather than during the increase in population density (Engel,
2000; Smetacek, 1985). In earlier studies we demonstrated that PCD-induced
demise in <italic>Trichodesmium</italic> is characterized by an increase in excreted
TEP (Berman-Frank et al., 2007) and enhanced sinking of particulate organic
matter (Bar-Zeev et al., 2013). TEP may be positively buoyant
(Azetsu-Scott and Passow, 2004), yet their stickiness causes aggregation and
clumping of cells and detritus, ultimately enhancing sinking rates of large
aggregates, including dying <italic>Trichodesmium</italic> (Bar-Zeev et al., 2013).</p>
</sec>
<sec id="Ch1.S4.SS1.SSS4">
  <?xmltex \opttitle{Changes in microbial community with \textit{Trichodesmium}
decline}?><title>Changes in microbial community with <italic>Trichodesmium</italic>
decline</title>
      <p>In the incubations, other diazotrophic populations succeeded the declining
<italic>Trichodesmium</italic> biomass as indicated by increasing N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation
rates, POC, and PON (Fig. 4b). In experiment 2, based on qPCR of targeted
diazotrophic phylotypes, the diazotroph community composition shifted from
being dominated by <italic>Trichodesmium</italic> spp. and unicellular groups
UCYN-A1, UCYN-A2, and UCYN-B (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>) to one dominated by diatom–diazotroph
associations Het-1 and Het-2 (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>72</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Bonnet et al., 2016b; K. Turk-Kubo,
personal communication, 2016). In experiment 1 heterotrophic bacteria thrived
and increased in abundance as the <italic>Trichodesmium</italic> biomass crashed
(Fig. 3).</p>
      <p><italic>Trichodesmium</italic> colonies host a wide diversity of microorganisms,
including specific epibionts, viruses, bacteria, eukaryotic microorganisms,
and metazoans (Hewson et al., 2009; Hmelo et al., 2012; Ohki, 1999; Paerl et
al., 1989; Sheridan et al., 2002; Siddiqui et al., 1992; Zehr, 1995).
Associated epibiont bacterial abundance in dilute and exponentially growing
laboratory cultures of <italic>Trichodesmium</italic> is relatively limited (Spungin
et al., 2014) compared to bloom conditions (Hewson et al., 2009; Hmelo et
al., 2012). Proliferation of <italic>Alteromonas</italic> and other <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">γ</mml:mi></mml:math></inline-formula>-Proteobacteria during biomass collapse (Fig. 3) confirms their reputation
as opportunistic microorganisms (Allers et al., 2008; Hewson et al., 2009;
Frydenborg et al., 2014; Pichon et al., 2013). Such organisms can thrive on
the influx of organic nutrient sources from the decaying
<italic>Trichodesmium</italic> as we observed (Fig. 3). Furthermore, the increase in
organic matter including TEP produced by the stressed <italic>Trichodesmium</italic>
(Figs. 1d and 4c) probably stimulated growth of these copiotrophs. Moreover,
as the <italic>Trichodesmium</italic> biomass declined in the carboys, the high
concentrations of NH<inline-formula><mml:math display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> (&gt; 5000 nmol L<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (Fig. 4b)
sustained both autotrophic and heterotrophic organisms (Berthelot et al.,
2015; Bonnet et al., 2016b, c). Thus, the increase in volumetric N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
fixation and PON that was measured in the incubation bottles right after the
<italic>Trichodesmium</italic> crash in experiment 2 (Fig. 4b) probably reflects both
the enhanced activity of other diazotrophs (see above and Bonnet et al.,
2016b) and the resistant residual <italic>Trichodesmium </italic>trichomes (Berman-Frank
et al., 2004) with increased cell-specific N<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fixation. This scenario is
consistent with the hypothesis that PCD induction and death of a fraction of
the population confers favorable conditions for survival and growth of
individual cells (Bidle and Falkowski, 2004; Bidle, 2015).</p>
</sec>
</sec>
<sec id="Ch1.S4.SS2">
  <title>Implications for the lagoon system and export flux</title>
      <p>Phytoplankton blooms and their dense surface accumulations occur under
favorable physical properties of the upper ocean (e.g., temperature,
mixed-layer depth, stratification) and specifically when division rates
exceed loss rates derived from grazing, viral attack, and sinking or export
from the mixed layer to depth (Behrenfeld, 2014). Although physical drivers
such as turbulence and mixing may scatter and dilute these dense
accumulations, the rapid disappearance of biomass in large sea-surface
<italic>Trichodesmium</italic> blooms (within 1–2 days in the lagoon waters) (Rodier
and Le Bourne, 2010) suggests loss of biomass by other mechanisms. The lack
of <italic>Trichodesmium</italic> developing within the VAHINE mesocosms and the
spatial–temporal variability in the surface bloom in the lagoon prohibited
in situ sampling of the same biomass for several days and prevented
conclusions regarding in situ mortality rates and export flux. Furthermore,
within these dense surface populations, as well as in the microcosm and
carboy experiments, Fe availability was probably extremely limited due to
high cellular demand and competition (Shaked, 2002). PCD induced by
Fe-depletion experiments with laboratory cultures and natural populations
results in rapid biomass demise, typically beginning after 24 h, with
&gt; 90 % of the biomass crashing 3 to 5 days after induction
(Bar-Zeev et al., 2013; Berman-Frank et al., 2004; Berman-Frank et al.,
2007). In similar experiments with P depletion, <italic>Trichodesmium</italic>
biomass did not crash rapidly. Rather, limitation induced colony formation
and elongation of trichomes (Spungin et al., 2014) and the cultures could be
sustained for another couple of weeks before biomass declined significantly
(unpublished data). The responses we quantified from the dying
<italic>Trichodesmium</italic> in the carboys and bottles (Figs. 3–7) were similar
to those obtained from controlled laboratory experiments where P and Fe
stress was validated individually. However, the rapid response here probably
reflects an exacerbated reaction due to the simultaneous combination of
different stressors and the presence of biotic components that can compete
for and utilize the organic resources (carbon, nitrogen, phosphorus)
generated by the dying <italic>Trichodesmium</italic>. In the lagoon, production of
TEP by stressed biomass combined with the degradation of gas vesicles and
enhanced aggregation will cause such surface accumulations or blooms to
collapse, leading to rapid vertical export of newly fixed nitrogen and carbon
in the ocean.</p>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions and implications</title>
      <p>We demonstrate that the rapid demise of a <italic>Trichodesmium</italic> surface
bloom in New Caledonia, with the disappearance of &gt; 90 % of
the biomass within 24 h in 4.5 L bottle incubations, displayed cellular
responses to P and Fe stress and was mediated by a suite of PCD genes. Virus
infection and lysis did not appear to directly cause the massive biomass
decline. Although virus infection may have modulated the cellular and genetic
responses to enhance PCD-driven loss processes, quorum sensing among
epibionts (Hmelo et al., 2012; Van Mooy et al., 2012), allelopathic
interactions, and the production of toxins by <italic>Trichodesmium</italic> (Guo and
Tester, 1994; Kerbrat et al., 2010) are additional factors that could be
important for a concerted response of the <italic>Trichodesmium</italic> population,
but we did not examine them here. Collectively, they would facilitate rapid
collapse and loss of <italic>Trichodesmium</italic> populations and possibly lead to
enhanced vertical fluxes and export production, as previously demonstrated in
PCD-induced laboratory cultures of <italic>Trichodesmium</italic> (Bar-Zeev et al.,
2013). We posit that PCD-induced demise, in response to concurrent cellular
stressors and facilitated by concerted gene regulation, is typical in natural
<italic>Trichodesmium</italic> blooms and leads to a high export production rather
than regeneration and recycling of biomass in the upper photic layers.</p>
</sec>
<sec id="Ch1.S6">
  <title>Data availability</title>
      <p>The raw transcriptomic data for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">8</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn>22</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> are available from
NCBI short read archive under the bioproject accession number PRJNA304389,
biosample accessions SAMN05207415, SAMN05207416, and SAMN05207417.</p>
</sec>

      
      </body>
    <back><app-group>
        <supplementary-material position="anchor"><p><bold>The Supplement related to this article is available online at <inline-supplementary-material xlink:href="http://dx.doi.org/10.5194/bg-13-4187-2016-supplement" xlink:title="pdf">doi:10.5194/bg-13-4187-2016-supplement</inline-supplementary-material>.</bold></p></supplementary-material>
        </app-group><notes notes-type="authorcontribution">

      <p>Ilana Berman-Frank, Dina Spungin, and Sophie Bonnet conceived and planned the
study. Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Wolfgang
R. Hess, Kay D. Bidle, and Ilana Berman-Frank participated in the experimental
sampling. Dina Spungin, Ulrike Pfreundt, Wolfgang R. Hess, Hugo Berthelot,
Frank Natale, Dina AlRoumi, Kay D. Bidle, and Ilana Berman-Frank analyzed the
samples and resulting data. Ilana Berman-Frank and Dina Spungin wrote the
manuscript with further contributions to the manuscript by Ulrike Pfreundt,
Wolfgang R. Hess, Sophie Bonnet, and Kay D. Bidle.</p>
  </notes><ack><title>Acknowledgements</title><p>Funding was obtained for Ilana Berman-Frank through a collaborative grant
from MOST Israel and the High Council for Science and Technology
(HCST), France, and a United States–Israel Binational Science Foundation (BSF)
grant (no. 2008048) to Ilana Berman-Frank and Kay D. Bidle. This research was
partially funded by the Gordon and Betty Moore Foundation through grant
GBMF3789 to KDB. The participation of Ilana Berman-Frank, Dina Spungin,
Ulrike Pfreundt, and Wolfgang R. Hess in the VAHINE experiment was supported
by the German-Israeli Research Foundation (GIF), project number
1133-13.8/2011 to Ilana Berman-Frank and Wolfgang R. Hess, and the
metatranscriptome analysis by the EU project MaCuMBA (Marine Microorganisms:
Cultivation Methods for Improving their Biotechnological Applications; grant
agreement no. 311975) to Wolfgang R. Hess. Funding for the VAHINE experimental
project was provided by the Agence Nationale de la Recherche (ANR starting
grant VAHINE ANR-13-JS06-0002), INSU-LEFE-CYBER program, GOPS, IRD, and MIO.
The authors thank the captain and crew of the R/V <italic>Alis</italic>, the SEOH
divers service from the IRD research center of Noumea (E. Folcher, B. Bourgeois, and
A. Renaud) and from the Observatoire Océanologique de
Villefranche-sur-mer (OOV, J. M. Grisoni), and the IRD
research center of Noumea for their helpful technical support. Thanks
especially to E. Rahav for his assistance throughout the New Caledonia
experiment and to H. Elifantz for assistance with the 16S sequencing and data
analysis. This work is in partial fulfillment of the requirements for a PhD
thesis for D. Spungin at Bar-Ilan University. We thank the three reviewers,
whose comments helped improve the manuscript substantially. <?xmltex \hack{\newline}?><?xmltex \hack{\newline}?> Edited by: D. G. Capone<?xmltex \hack{\newline}?> Reviewed by: three
anonymous referees</p></ack><ref-list>
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    <!--<article-title-html>Mechanisms of <i>Trichodesmium</i> demise within the New Caledonian lagoon during the VAHINE
mesocosm experiment</article-title-html>
<abstract-html><p class="p">The globally important marine diazotrophic cyanobacterium
<i>Trichodesmium</i> is abundant in the New Caledonian lagoon (southwestern
Pacific Ocean) during austral spring/summer. We investigated the cellular
processes mediating <i>Trichodesmium</i> mortality from large surface
accumulations (blooms) in the lagoon. <i>Trichodesmium</i> cells (and
associated microbiota) were collected at the time of surface accumulation,
enclosed under simulated ambient conditions, and sampled over time to
elucidate the stressors and subcellular underpinning of rapid biomass demise
(&gt; 90 % biomass crashed within  ∼  24 h).
Metatranscriptomic profiling of <i>Trichodesmium</i> biomass, 0, 8 and
22 h after incubations of surface accumulations, demonstrated upregulated
expression of genes required to increase phosphorus (P) and iron (Fe)
availability and transport, while genes responsible for nutrient storage were
downregulated. Total viral abundance oscillated throughout the experiment and
showed no significant relationship with the development or demise of the
<i>Trichodesmium</i> biomass. Enhanced caspase-specific activity and
upregulated expression of a suite of metacaspase genes, as the
<i>Trichodesmium</i> biomass crashed, implied autocatalytic programmed cell
death (PCD) as the mechanistic cause. Concurrently, genes associated with
buoyancy and gas vesicle production were strongly downregulated concomitant
with increased production and high concentrations of transparent exopolymeric
particles (TEP). The rapid, PCD-mediated, decline of the
<i>Trichodesmium</i> biomass, as we observed from our incubations,
parallels mortality rates reported from <i>Trichodesmium</i> blooms in
situ. Our results suggest that, whatever the ultimate factor, PCD-mediated
death in <i>Trichodesmium</i> can rapidly terminate blooms, facilitate
aggregation, and expedite vertical flux to depth.</p></abstract-html>
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