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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Mar. Sci.</journal-id>
<journal-title>Frontiers in Marine Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Mar. Sci.</abbrev-journal-title>
<issn pub-type="epub">2296-7745</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fmars.2024.1341619</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Marine Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Diel variation of seawater volatile organic compounds, DMSP-related compounds, and microbial plankton inside and outside a tropical coral reef ecosystem</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Masdeu-Navarro</surname>
<given-names>Marta</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author">
<name>
<surname>Mangot</surname>
<given-names>Jean-Fran&#xe7;ois</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author">
<name>
<surname>Xue</surname>
<given-names>Lei</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
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<contrib contrib-type="author">
<name>
<surname>Cabrera-Brufau</surname>
<given-names>Miguel</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author">
<name>
<surname>Kieber</surname>
<given-names>David J.</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
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<contrib contrib-type="author">
<name>
<surname>Rodr&#xed;guez-Ros</surname>
<given-names>Pablo</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
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<contrib contrib-type="author">
<name>
<surname>Gardner</surname>
<given-names>Stephanie G.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
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<contrib contrib-type="author">
<name>
<surname>Bergauer</surname>
<given-names>Kristin</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Herndl</surname>
<given-names>Gerhard J.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
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<contrib contrib-type="author">
<name>
<surname>Marras&#xe9;</surname>
<given-names>C&#xe8;lia</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author" corresp="yes">
<name>
<surname>Sim&#xf3;</surname>
<given-names>Rafel</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
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<aff id="aff1">
<sup>1</sup>
<institution>Institut de Ci&#xe8;ncies del Mar (ICM-CSIC)</institution>, <addr-line>Barcelona, Catalonia</addr-line>, <country>Spain</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Department of Chemistry, College of Environmental Science and Forestry, State University of New York</institution>, <addr-line>Syracuse, NY</addr-line>, <country>United States</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna</institution>, <addr-line>Vienna</addr-line>, <country>Austria</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research</institution>, <addr-line>Den Burg</addr-line>, <country>Netherlands</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Christian L&#xf8;nborg, Aarhus University, Denmark</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: V&#xed;ctor Fern&#xe1;ndez-Ju&#xe1;rez, University of Copenhagen, Denmark</p>
<p>Jonathan David Todd, University of East Anglia, United Kingdom</p>
<p>Graham Barry Jones, Southern Cross University, Australia</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Rafel Sim&#xf3;, <email xlink:href="mailto:rsimo@icm.csic.es">rsimo@icm.csic.es</email>
</p>
</fn>
<fn fn-type="present-address" id="fn003">
<p>&#x2020;Present addresses: Pablo Rodr&#xed;guez-Ros, Marilles Foundation, Palma, Mallorca, Illes Balears, Spain; Stephanie G. Gardner, School of Life and Environmental Sciences, The University of Sydney, NSW, Australia; Kristin Bergauer, Ocean Ecosystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>16</day>
<month>02</month>
<year>2024</year>
</pub-date>
<pub-date pub-type="collection">
<year>2024</year>
</pub-date>
<volume>11</volume>
<elocation-id>1341619</elocation-id>
<history>
<date date-type="received">
<day>20</day>
<month>11</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>30</day>
<month>01</month>
<year>2024</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2024 Masdeu-Navarro, Mangot, Xue, Cabrera-Brufau, Kieber, Rodr&#xed;guez-Ros, Gardner, Bergauer, Herndl, Marras&#xe9; and Sim&#xf3;</copyright-statement>
<copyright-year>2024</copyright-year>
<copyright-holder>Masdeu-Navarro, Mangot, Xue, Cabrera-Brufau, Kieber, Rodr&#xed;guez-Ros, Gardner, Bergauer, Herndl, Marras&#xe9; and Sim&#xf3;</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Biogenic volatile organic compounds (VOCs) play key roles in coral reef ecosystems, where, together with dimethylated sulfur compounds, they are indicators of ecosystem health and are used as defense strategies and infochemicals. Assessment and prediction of the exchange rates of VOCs between the oceans and atmosphere, with implications for atmospheric reactivity and climate, are hampered by poor knowledge of the regulating processes and their temporal variability, including diel cycles. Here, we measured the variation over 36h of the concentrations of DMSPCs (dimethylsulfoniopropionate (DMSP)-related compounds, namely DMSP, dimethylsulfoxide, acrylate, dimethylsulfide, and methanethiol as dimethyl disulfide) and VOCs (COS, CS<sub>2</sub>, isoprene, the iodomethanes CH<sub>3</sub>I and CH<sub>2</sub>ClI, and the bromomethanes CHBr<sub>3</sub> and CH<sub>2</sub>Br<sub>2</sub>), in surface waters inside the shallow, northern coral-reef lagoon of Mo&#x2019;orea (French Polynesia) and 4&#xa0;km offshore, in the tropical open ocean. Comparisons with concurrent measurements of sea surface temperature, solar radiation, biogeochemical variables (nutrients, organic matter), and the abundances and taxonomic affiliations of microbial plankton were conducted with the aim to explain interconnections between DMSPCs, VOCs, and their environment across diel cycles. In open ocean waters, deeper surface mixing and low nutrient levels resulted in low phytoplankton biomass and bacterial activity. Consequently, the diel patterns of VOCs were more dependent on photochemical reactions, with daytime increases for several compounds including dissolved dimethylsulfoxide, COS, CS<sub>2</sub>, CH<sub>3</sub>I, and CH<sub>2</sub>ClI. A eukaryotic phytoplankton assemblage dominated by dinoflagellates and haptophytes provided higher cell-associated DMSP concentrations, yet the occurrence of DMSP degradation products (dimethylsulfide, dimethyl disulfide) was limited by photochemical loss. Conversely, in the shallow back reef lagoon the proximity of seafloor sediments, corals and abundant seaweeds resulted in higher nutrient levels, more freshly-produced organic matter, higher bacterial activity, and larger algal populations of <italic>Mamiellales</italic>, diatoms and <italic>Cryptomonadales</italic>. Consequently, DMSP and dimethylsulfoxide concentrations were lower but those of most VOCs were higher. A combination of photobiological and photochemical processes yielded sunny-daytime increases and nighttime decreases of dimethylsulfide, dimethyl disulfide, COS, isoprene, iodomethanes and bromomethanes. Our results illustrate the important role of solar radiation in DMSPC and VOC cycling, and are relevant for the design of sampling strategies that seek representative and comparable measurements of these compounds.</p>
</abstract>
<kwd-group>
<kwd>coral reef</kwd>
<kwd>Mo&#x2019;orea</kwd>
<kwd>tropical ocean</kwd>
<kwd>diel cycles</kwd>
<kwd>DMSP</kwd>
<kwd>VOC</kwd>
<kwd>solar radiation</kwd>
<kwd>microorganisms</kwd>
</kwd-group>
<counts>
<fig-count count="6"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="126"/>
<page-count count="17"/>
<word-count count="9108"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Marine Biogeochemistry</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Marine environments produce and emit volatile organic compounds (VOCs) mainly through biological and photochemical processes. Ocean-leaving VOCs participate in the regulation of atmospheric oxidative capacity and aerosol formation and growth in the low marine atmosphere (<xref ref-type="bibr" rid="B10">Carpenter et&#xa0;al., 2012</xref>). In the tropical oceans, furthermore, strong and deep convection rapidly transports ocean-emitted VOCs from the boundary layer to the upper troposphere and even the stratosphere, where they participate in ozone destruction and new aerosol formation (<xref ref-type="bibr" rid="B24">Fuhlbr&#xfc;gge et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B71">Lennartz et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B120">Williamson et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B23">Filus et&#xa0;al., 2020</xref>).</p>
<p>Tropical coral reefs are highly productive ecosystems in oligotrophic oceans (<xref ref-type="bibr" rid="B41">Hoegh-Guldberg et&#xa0;al., 2017</xref>) that harbor around 30% of all marine species (<xref ref-type="bibr" rid="B64">Knowlton et&#xa0;al., 2010</xref>). Scleractinian or stony corals, which form massive calcium carbonate skeletons, are the main builders of coral reefs, where they provide habitats to a variety of life forms, from vertebrate and invertebrate animals to seaweeds and planktonic and benthic microbes. Active recycling of nutrients in the entire ecosystem allows coral reefs to remain productive, provide ecological niches, and contribute to regional biogeochemical cycles. Coral reef ecosystems produce multiple VOCs (<xref ref-type="bibr" rid="B21">Exton et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>) that are indicators of the ecosystem state and chemical cues for organism interactions and/or defense strategies. It has been suggested that coral reefs are hot spots of VOC production and emission, but the evidence is limited (<xref ref-type="bibr" rid="B21">Exton et&#xa0;al., 2015</xref>), and the statement cannot be generalized (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>).</p>
<p>Only a few studies have characterized the VOC composition of reef ecosystems beyond dimethylsulfide (DMS) and isoprene (<xref ref-type="bibr" rid="B68">Lawson et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B67">2021</xref>; <xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>), and knowledge of their sources is largely uneven across compounds. Isoprene (C<sub>5</sub>H<sub>8</sub>) is produced by phytoplankton (<xref ref-type="bibr" rid="B81">McGenity et&#xa0;al., 2018</xref>) and tropical coral holobionts (<xref ref-type="bibr" rid="B112">Swan et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B16">Dawson et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B67">Lawson et&#xa0;al., 2021</xref>); whether its production results from thermal stress, as is the case with vascular plants on land (<xref ref-type="bibr" rid="B73">Loreto and Schnitzler, 2010</xref>; <xref ref-type="bibr" rid="B81">McGenity et&#xa0;al., 2018</xref>), is unknown. Halomethanes (halogenated C1 compounds) are also produced by phytoplankton and consequently ubiquitous in the surface ocean, but they typically occur at much higher concentrations in coastal waters, where they are produced by seaweeds in response to oxidative stress and as part of defense mechanisms (<xref ref-type="bibr" rid="B10">Carpenter et&#xa0;al., 2012</xref>). Amongst volatile sulfur compounds, carbonyl sulfide (COS) is mostly generated by the interaction of solar radiation with dissolved organic matter (<xref ref-type="bibr" rid="B116">Uher and Andreae, 1997</xref>; <xref ref-type="bibr" rid="B70">Lennartz et&#xa0;al., 2020</xref>). Carbon disulfide (CS<sub>2</sub>) is thought to be produced by hypoxic sediments at the seafloor and photochemical reactions in sunlit waters, yet the mechanisms are not well characterized (<xref ref-type="bibr" rid="B61">Kim and Andreae, 1992</xref>; <xref ref-type="bibr" rid="B70">Lennartz et&#xa0;al., 2020</xref>). More is known about DMS and its pervasive biochemical precursor, the non-volatile compound dimethylsulfoniopropionate (DMSP). Marine environments, including coral reefs, are sources of DMSP because many microalgal taxa, including both phytoplankton and the coral endosymbionts Symbiodiniaceae, synthesize vast amounts of DMSP as a cellular osmolyte and antioxidant (<xref ref-type="bibr" rid="B18">Deschaseaux et&#xa0;al., 2014</xref>), and so do some cnidarians (<xref ref-type="bibr" rid="B94">Raina et&#xa0;al., 2013</xref>) and their associated bacteria (<xref ref-type="bibr" rid="B65">Kuek et&#xa0;al., 2022</xref>). DMSP can undergo enzymatic cleavage, resulting in the formation of DMS and acrylate. This catabolic pathway is believed to play a pivotal role in mitigating oxidative stress (<xref ref-type="bibr" rid="B111">Sunda et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B82">McParland et&#xa0;al., 2021</xref>). An alternative, often preferential, catabolic process involves demethylation and demethiolation, leading to the assimilation of sulfur by the consumer and the release of methanethiol (MeSH) as a by-product (<xref ref-type="bibr" rid="B60">Kiene et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B44">Howard et&#xa0;al., 2006</xref>). Subsequent oxidation of DMS and MeSH gives rise to dimethylsulfoxide (DMSO) and dimethyldisulfide (DMDS), respectively (<xref ref-type="bibr" rid="B59">Kiene, 1996</xref>; <xref ref-type="bibr" rid="B17">Del Valle et&#xa0;al., 2007</xref>). DMSO can also be produced by cleavage of dimethylsulfoxonium propionate (DMSOP), a metabolite produced by intracellular oxidation of DMSP (<xref ref-type="bibr" rid="B114">Thume et&#xa0;al., 2018</xref>). The suite of DMSP, DMS, MeSH, DMDS, acrylate and DMSO can be collectively named DMSP-related compounds (DMSPCs).</p>
<p>Even though solar radiation represents a fundamental driver for the production and cycling of many VOCs and DMSPCs (<xref ref-type="bibr" rid="B10">Carpenter et&#xa0;al., 2012</xref>), changes in the concentrations of these compounds over diel cycles are largely unknown. Very few studies have addressed diel cycles in any marine ecosystem, including the open ocean, and they have mainly focused on DMSPCs (<xref ref-type="bibr" rid="B6">Broadbent and Jones, 2006</xref>; <xref ref-type="bibr" rid="B27">Gal&#xed; et&#xa0;al., 2013b</xref>; <xref ref-type="bibr" rid="B99">Royer et&#xa0;al., 2016</xref>). Diel variations are expected in coral reefs because of the high densities of light-sensitive organisms. Coral holobiont physiology changes in response to incident solar radiation and circadian rhythms (<xref ref-type="bibr" rid="B36">Hemond and Vollmer, 2015</xref>), and switches from daytime autotrophy, when the algal symbionts fix carbon and produce oxygen, to nighttime heterotrophy, when polyps prey on plankton (<xref ref-type="bibr" rid="B40">Hoadley et&#xa0;al., 2021</xref>) and animal respiration is higher due to digestion (<xref ref-type="bibr" rid="B103">Schneider et&#xa0;al., 2009</xref>). In a previous paper (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>), we reported for the first time the diel patterns of VOCs and DMSPCs in the close vicinity (1-2&#xa0;cm) and 2&#xa0;m away from a patch of the coral <italic>Acropora pulchra</italic> in a reef at the NW coast of Mo&#x2019;orea, French Polynesia. We showed that the coral holobiont was a strong source of DMSPCs, with large daytime release suggesting that these compounds arose from solar radiation stress. Conversely, the coral was a weaker or null source of other volatile sulfur compounds, isoprene and halomethanes. Here we investigated the short-term variations of VOCs and DMSPCs concentrations over day and night in the lagoon waters of another Mo&#x2019;orean reef and compare it with the short-term variations in the neighboring open ocean. We hypothesized that (a) microbial plankton and solar radiation govern the presence and dynamics of VOCs and DMSPCs in the open ocean, while in the back reef these compounds are also controlled by corals, seaweeds, sediments, and photochemical reactions with freshly produced organic matter; (b) in both cases, solar radiation plays a pivotal role, resulting in recognizable diel patterns for these compounds. Our overarching goal was to shed light on the origin of these compounds in tropical marine ecosystems, their short-term variability, and their dependence on sunlight.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="s2_1">
<title>Study area</title>
<p>Fieldwork was conducted in the northern coast of the island of Mo&#x2019;orea, French Polynesia (17&#xb0;29&#x2019;00.0&#x201d;S 149&#xb0;50&#x2019;00.0&#x201d;W), between 12th and 20th of April 2018. Surface water was collected at two sampling sites: one located 4&#xa0;km offshore in the open ocean (OO) over a bathymetric depth of 1200&#xa0;m; and the other located in the back-reef (BR) lagoon, over a depth of &#x223c;2.5 m. The northern reefs of Moorea have shallow depths (0.5-3&#xa0;m; <xref ref-type="bibr" rid="B69">Leichter et&#xa0;al., 2013</xref>) and are characterized by patches of <italic>Pocillopora</italic> spp., <italic>Acropora</italic> spp. and other corals on a sandy bottom, and partly covered by the brown seaweed <italic>Turbinaria ornata</italic> (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>).</p>
</sec>
<sec id="s2_2">
<title>Sample collection and storage</title>
<p>At each of the two sites, seawater samples were collected every 6&#xa0;h over a period of 34&#xa0;h on April 12-13 (BR) and April 19-20 (OO) from the surface (0-50&#xa0;cm) using a small boat. Sampling times were 04:00, 10:00, 16:00, 22:00, 04:00, 10:00, and 14:00 (13:00 at OO) local time. Logistical and personnel limitations prevented extending the sampling to another 24-h cycle, which would have been desirable to ensure that the observed patterns were repeated. For VOCs, DMSPCs, and dissolved organic carbon and nitrogen (DOC, DON), samples were collected using acid-cleaned 0.5 L glass bottles rinsed three times and filled to the brim by hand. For other biogeochemical variables, cell counts and 16S and 18S genes rRNA metabarcoding, water was withdrawn with a peristaltic pump into an acid-cleaned and pre-rinsed Teflon-lined plastic carboy (20 L), while filtered through a 200 &#x3bc;m mesh to remove large particles and organisms. Samples were maintained in a water bath continuously flushed with surface seawater, in dimmed light, until processing in the UC Berkeley Gump laboratory on the island ca. 1&#xa0;h after collection.</p>
</sec>
<sec id="s2_3">
<title>VOC and DMSPC concentrations</title>
<p>Dissolved VOCs were quantified within 3&#xa0;h of sample collection by purge and trap gas chromatography-mass spectrometry as described previously (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>). Target VOCs were COS, DMS, CS<sub>2</sub>, DMDS, isoprene, CH<sub>3</sub>I, CH<sub>2</sub>ClI, CH<sub>2</sub>Br<sub>2</sub>, CHBr<sub>3</sub>. Each sample was analyzed in duplicate. Limits of detection for a 25 ml sample, including correction for blanks, were 2 pM COS, CS<sub>2</sub>, DMDS and isoprene, 15 pM DMS, 0.6 pM CH<sub>3</sub>I, 0.2 pM CH<sub>2</sub>ClI, 1.5 pM CH<sub>2</sub>Br<sub>2</sub> and CHBr<sub>3</sub>. For total DMSP (DMSP<sub>t</sub>) 35% HCl (10 mL per mL of sample) was added to unfiltered samples followed by storage at room temperature in the dark. To determine dissolved concentrations of DMSP (DMSP<sub>d</sub>), acrylate and DMSO, 15&#xa0;ml sample aliquots were gravity filtered using precombusted 25&#xa0;mm diameter Whatman glass-fiber (GF/F) filters into 20&#xa0;ml scintillation vials. Filtrates were microwaved to boiling, bubbled with high-purity nitrogen gas to remove DMS, and acidified (<xref ref-type="bibr" rid="B62">Kinsey and Kieber, 2016</xref>). Back in our home lab, DMSP<sub>t</sub> and DMSP<sub>d</sub> were determined as evolved DMS by purge and trap gas chromatography with flame photometric detection, after alkaline hydrolysis. DMSO was determined as evolved DMS after reduction with TiCl<sub>3</sub>. Acrylate concentrations were determined using a pre-column derivatization HPLC method (<xref ref-type="bibr" rid="B115">Tyssebotn et&#xa0;al., 2017</xref>). The particulate forms of the three compounds (DMSP<sub>p</sub>, DMSO<sub>p</sub> and acrylate<sub>p</sub>) were determined by subtracting the dissolved from the total form. All analyses were run in duplicate.</p>
</sec>
<sec id="s2_4">
<title>Sea surface temperature, chlorophyll <italic>a</italic>, nutrients, DOC, DON, POC, PON, and FDOM</title>
<p>The sea surface temperature (SST) was recorded on the boat with an SBE56 sensor (Sea-Bird Sci.) continuously flushed with pumped surface seawater.</p>
<p>For determination of chlorophyll <italic>a</italic> (Chla) concentrations, duplicate 250 mL aliquots of unfiltered seawater were taken from the sample carboys, filtered through 25&#xa0;mm diameter GF/F filters and stored at -20&#xb0;C until analysis. Chla extraction was performed in 90% acetone at 4&#xb0;C for 24&#xa0;h. The fluorescence of the extracts was measured with a calibrated Turner Designs fluorometer (model 10-AU-005 field fluorometer) equipped with an excitation and emission filters at 340-500 nm and above 665 nm, respectively.</p>
<p>For particulate organic carbon (POC) and particulate organic nitrogen (PON) analyses, 1.5 L seawater aliquots were taken from the carboys, filtered through precombusted (450&#xb0;C for 4h) GF/F filters and stored frozen at -20&#xb0;C until analysis. Filters for POC determination were decarbonated with acid vapor (<xref ref-type="bibr" rid="B125">Yamamuro and Kayanne, 1995</xref>). No replicates were analyzed. Carbon and nitrogen were determined with an elemental analyzer (Perkin-Elmer 2400 CHN). For the determination of total organic carbon (TOC) and total nitrogen (TN), unfiltered seawater aliquots (30 mL) were collected in acid-cleaned polycarbonate bottles and immediately stored at -20&#xb0;C until analysis. Carbon and nitrogen were determined after inorganic C removal through acidification using a Shimadzu TOC VCSH instrument. Analytical quadruplicates were run. The equipment was calibrated with potassium hydrogen phthalate. High-purity laboratory water obtained from a MilliporeSigma Milli Q system (MilliQ water) was used as a blank and the reference material used was deep Sargasso Sea water (MRC Batch-15 Lot//11-15, measured TOC: 43.2 &#xb1; 1.1 &#xb5;M, Dr. Dennis Hansell Laboratory, University of Miami, RSMAS). Dissolved organic carbon (DOC) concentrations were calculated by subtracting POC concentrations from TOC. Samples (10 mL) for inorganic nutrient determination were collected unfiltered and stored at -20&#xb0;C until analysis. Concentrations of nitrate (NO<sub>3</sub>
<sup>-</sup>), nitrite (NO<sub>2</sub>
<sup>-</sup>), ammonia (NH<sub>4</sub>
<sup>+</sup>), phosphate (PO<sub>4</sub>
<sup>3-</sup>) and silicate (SiO<sub>4</sub>
<sup>2-</sup>) were determined with an auto-analyzer (Bran Luebbe AA3) with spectrophotometric detection (<xref ref-type="bibr" rid="B32">Grasshoff, 1978</xref>). No replicates were analyzed. Dissolved organic nitrogen (DON) concentrations were calculated by subtracting inorganic nitrogen (nitrate, nitrite and ammonia) and PON concentrations from TN.</p>
<p>Characterization of fluorescent dissolved organic matter (FDOM) was performed with a Horiba Aqualog spectrofluorometer. Briefly, ca. 4 mL seawater aliquots were filtered through pre-combusted (450&#xb0;C for 4 hours) GF/F filters. Fluorescence was recorded as square excitation-emission matrices in the 240-600 nm range. One to four analytical replicates were run. The intensity of peak T (hereafter referred to as FDOM-T), as defined by <xref ref-type="bibr" rid="B14">Coble (1996)</xref>, was extracted as the fluorescence at excitation/emission wavelengths 275/340 nm using the <italic>staRdom</italic> package (<xref ref-type="bibr" rid="B92">Pucher et&#xa0;al., 2019</xref>). Fluorescence intensity is presented in Raman Units (RU) after normalization to the Raman scatter measured in MilliQ water blanks (<xref ref-type="bibr" rid="B66">Lawaetz and Stedmon, 2009</xref>).</p>
</sec>
<sec id="s2_5">
<title>Microorganism abundances and bacterial production</title>
<p>For the enumeration of heterotrophic prokaryotes (including bacteria and archaea) and pico- and nano-phytoplankton, 2-5 mL sample aliquots were fixed with glutaraldehyde (0.5%) and stored at &#x2212;80&#xb0;C until analysis based on size and fluorescence on a flow cytometer capable of true volumetric absolute counting (CyFlow Cube 8, Sysmex Partec). Heterotrophic prokaryotes were stained with SYBRgreen I (&#x223c;20 &#xb5;M final concentration) prior to quantification using green fluorescence. Prokaryotic (i.e., <italic>Synechococcus</italic> and <italic>Prochlorococcus</italic>) and eukaryotic pico- and nanophytoplankton were counted based on red and orange autofluorescence (<xref ref-type="bibr" rid="B28">Gasol and del Giorgio, 2000</xref>). No replicates were analyzed.</p>
<p>For bacterial biomass production estimates, 1 L of seawater was collected in acid cleaned amber bottles and stored at ambient temperature until further processing. The biomass production of the bacterial community was determined as described in <xref ref-type="bibr" rid="B22">Fadeev et&#xa0;al. (2023)</xref>, based on the single-cell incorporation of L-homopropargylglycine (HPG) into newly synthesized bacterial proteins (<xref ref-type="bibr" rid="B101">Samo et&#xa0;al., 2014</xref>). Briefly, seawater samples were amended with 50 &#x3bc;M HPG (final concentration of 20 nM) and incubated at <italic>in situ</italic> temperatures in the dark for 6&#xa0;h. Afterwards, samples were fixed with formaldehyde (2-4% final concentration) at 4&#x2da;C for at least 1&#xa0;h in the dark and stored at -20&#x2da;C until further processing. Prior to the microscopic analysis, the samples were stained with 2 &#xb5;g mL-1 4&#x2032;,6-diamidino-2-phenylindole (DAPI) in Vectashield (Vector Laboratories, Newark, CA, USA). The cells were enumerated using a Zeiss Axio Imager M2 epifluorescence microscope (Carl Zeiss AG, Oberkochen, Germany) at 1250&#xd7; magnification and the DAPI (Ex/Em = 358/461 nm) and the FITC (Ex/Em = 495/519 nm) filter sets. The bacterial abundance was calculated based on the average number of cells from at least 20 counting fields with 20-200 cells enumerated per counting field. At least 20 fields were counted for each filter slice using the Automated Cell Measuring and Enumeration Tool (ACMETool2, M. Zeder, Technobiology GmbH, Buchrain, Switzerland). The total abundance of biomass producing cells was determined as simultaneous signal of DAPI and FITC channels.</p>
</sec>
<sec id="s2_6">
<title>Solar radiation</title>
<p>Global solar radiation (W/m<sup>2</sup>) data were provided by the meteorological station at the Gump Research Station (<xref ref-type="bibr" rid="B119">Washburn and Brooks, 2022</xref>), located 1.5&#xa0;km and 5&#xa0;km away from the sampling sites BR and OO, respectively.</p>
</sec>
<sec id="s2_7">
<title>16S/18S rRNA gene amplicon sequencing and processing</title>
<p>Single seawater aliquots (2 L, no replicates) for DNA collection were taken from the sampled carboys and filtered through 47&#xa0;mm diameter polycarbonate filters of 0.2 &#x3bc;m pore size using a peristaltic pump. DNA filters were flash-frozen in liquid nitrogen and subsequently stored at &#x2212;80&#xb0;C. DNA extractions were performed using a standard phenol chloroform protocol (<xref ref-type="bibr" rid="B79">Massana et&#xa0;al., 1997</xref>) with a final step of purification using ultrafiltration in Amicon units (Millipore). Prokaryotic and eukaryotic diversity was determined by amplicon sequencing of the V4/V5 and V4 regions of the 16S and 18S rRNA genes, respectively, using the Illumina MiSeq platform and paired-end reads (2 &#xd7; 250 bp). PCR amplifications were performed using (1) the prokaryotic universal primers 515F-Y (5&#x2019;-GTGYCAGCMGCCGCGGTAA-3&#x2019;) and 926R (5&#x2019;-CCGYCAATTYMTTTRAGTTT-3&#x2019;) (<xref ref-type="bibr" rid="B89">Parada et&#xa0;al., 2016</xref>) and (2) the eukaryotic universal primers V4F (5&#x2019;-CCA GCA SCY GCG GTAATT CC-3&#x2019;) and V4R (5&#x2019;-ACTTTC GTT CTT GAT YRR-3&#x2019;) (<xref ref-type="bibr" rid="B5">Balzano et&#xa0;al., 2015</xref>). All samples were sequenced at Research and Testing Laboratories (RTL, Lubbock, TX, USA) using the Illumina MiSeq platform (2 &#xd7; 250 bp paired&#x2010;end sequencing).</p>
<p>Illumina reads were processed as described in <xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al. (2022)</xref>. Briefly, raw reads from both 16S and 18S rRNA gene sets were trimmed to remove amplification primers and spurious sequences using cutadapt v2.3 (<xref ref-type="bibr" rid="B76">Martin, 2011</xref>) and subsequently processed with DADA2 v1.4 (<xref ref-type="bibr" rid="B9">Callahan et&#xa0;al., 2016</xref>) to differentiate the 16S/18S rRNA gene amplicon sequence variants (ASVs) and to remove chimeras. ASVs were taxonomically assigned using the Ribosomal Database Project na&#xef;ve Bayesian classifier (<xref ref-type="bibr" rid="B118">Wang et&#xa0;al., 2007</xref>), as implemented in DADA2, and an 80% minimum bootstrap confidence threshold using SILVA (v132; (<xref ref-type="bibr" rid="B91">Pruesse et&#xa0;al., 2007</xref>)) and PR2 (v4.11.1; (<xref ref-type="bibr" rid="B33">Guillou et&#xa0;al., 2013</xref>)) as reference databases for the 16S and 18S rRNA sets, respectively. Singletons and sequences affiliated to eukaryotes, organelles, or chloroplasts (for the 16S rRNA set) or to metazoans, Embryophyceae, Rhodophyta, Ulveophyceae or Phaeophyceae (for the 18S rRNA set) were removed.</p>
<p>To compare samples, ASV tables were randomly subsampled down to the minimum number of reads per sample for both rDNA sets (17,694 and 3,203 reads for the 16S and 18S rDNA sets, respectively) using the rarefy function in the vegan v2.5.7 package (<xref ref-type="bibr" rid="B86">Oksanen et&#xa0;al., 2021</xref>) in R v4.0.2 (<xref ref-type="bibr" rid="B97">R Development Core Team, 2021</xref>). The final ASV tables contained 2,018 prokaryotic ASVs and 1,473 protistan ASVs.</p>
<p>To gain insight into the diversity and temporal variation of the phototrophic eukaryotic assemblage (namely, autotrophs and mixotrophs), protistan ASVs were classified into four major functional groups on the basis of their taxonomic affiliation: autotrophs (obligate phototrophs), heterotrophs (mainly predators), mixotrophs, and parasites (including saprobes), based on previous works relative to the annotation into functional traits of protistan diversity (<xref ref-type="bibr" rid="B30">Genitsaris et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B29">2016</xref>; <xref ref-type="bibr" rid="B95">Ramond et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B96">2019</xref>; <xref ref-type="bibr" rid="B83">Minicante et&#xa0;al., 2019</xref>). ASV assigned at poor taxonomic resolution (e.g., unclassified Dinophyceae) or to a family/order of organisms that include both autotrophs and heterotrophs (e.g., Gymnodiniaceae) were not attributed to any specific functional groups and were annotated as &#x2018;not determined (ND)&#x201d;. A detailed list of the classification for each protistan taxa is available in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>.</p>
</sec>
<sec id="s2_8">
<title>Data analysis</title>
<p>Statistical difference between the data series from both sampling sites (BR and OO) was evaluated with a non-parametric Kruskal-Wallis test. Spatial differences between the microbial community structure at each site obtained from the metabarcoding gene analysis were visualized using nonmetric multidimensional scaling (NMDS) based on Bray-Curtis distances and were obtained using the metaMDS function of the vegan R package. To investigate the relationships between VOCs and DMSPCs, and between these compounds and solar radiation, pairwise Spearman&#x2019;s correlations were computed with the ggcor v0.9&#x2013;7 package in R (<xref ref-type="bibr" rid="B43">Houyun et&#xa0;al., 2020</xref>). Due to the short data series used (n=7), the threshold for correlation significance was set at p&lt;0.1.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results and discussion</title>
<sec id="s3_1">
<title>Diel variation of environmental variables and microbial abundances</title>
<sec id="s3_1_1">
<title>Environmental variables</title>
<p>While solar radiation was similar at the two stations for the first respective sampling day, it was cloudy on the second sampling day at BR with substantially less solar radiation compared to that on the second sampling day at OO (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). The sea surface temperature (SST) showed a similar average at both sites (Kruskal-Wallis p&gt;0.05) and stronger diel variation at OO (28.7 &#xb1; 0.3&#xb0;C in BR, 27.7 &#xb1; 1.5&#xb0;C in OO) (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). This similarity despite the enormous difference in water column depth (2.5&#xa0;m in BR, 1200&#xa0;m in OO) highlights the strong connectivity of the two sampling sites. Indeed, the water flow across the reef is largely unidirectional: open ocean water enters the reef by wave action over the crest, flows across the back reef lagoon and exits the reef along the lagoon channel into Paopao Bay reef pass, where it flows out into the open ocean (<xref ref-type="bibr" rid="B37">Hench et&#xa0;al., 2008</xref>). Based on current speeds, the estimated residence time of seawater in the back reef lagoon is only a few hours, which is not sufficient to significantly warm it up. Nonetheless, the effect of weak tides and reef topography, where coral colonies can trap and recirculate waters in their wakes (<xref ref-type="bibr" rid="B38">Hench and Rosman, 2013</xref>), may complicate this speed-based estimate, resulting in a diel cycle of SST at BR that is less noticeable than that at OO (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). In comparison to OO waters, the lagoon waters (BR) contained higher concentrations of Chla (0.25 &#xb1; 0.09 vs 0.11&#xb1; 0.01 &#x3bc;g/L; Kruskal-Wallis p&lt;0.01), nitrate (0.33 &#xb1; 0.08 vs 0.03 &#xb1; 0.01 &#x3bc;M; Kruskal-Wallis p&lt;0.01), nitrite (0.049 &#xb1; 0.005 vs 0.011 &#xb1; 0.002 &#x3bc;M; Kruskal-Wallis p&lt;0.01), phosphate (0.16 &#xb1; 0.01 vs 0.12 &#xb1; 0.01 &#x3bc;M; Kruskal-Wallis p&lt;0.01), silicate (0.93 &#xb1; 0.04 vs 0.80 &#xb1; 0.05 &#x3bc;M; Kruskal-Wallis p&lt;0.01), and FDOM-T (0.017 &#xb1; 0.003 vs 0.011 &#xb1; 0.001 RU; Kruskal-Wallis p&lt;0.01) (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1B&#x2013;H</bold>
</xref>), suggesting there were additional reef or coastal (e.g., groundwater discharges; <xref ref-type="bibr" rid="B34">Ha&#xdf;ler et&#xa0;al., 2019</xref>) sources for these variables. Conversely, DOC concentrations were lower at BR (68.9 &#xb1; 4.2 vs 73.1 &#xb1; 1.4 &#x3bc;M; Kruskal-Wallis p&lt;0.05), and DON (4.1 &#xb1; 0.3 vs 4.1 &#xb1; 0.5 &#x3bc;M; Kruskal-Wallis p&gt;0.05), POC (3.5 &#xb1; 0.6 vs 3.2 &#xb1; 0.4 &#x3bc;M; Kruskal-Wallis p&gt;0.05) and PON (0.32 &#xb1; 0.07 vs 0.29 &#xb1; 0.07 &#x3bc;M; Kruskal-Wallis p&gt;0.05) concentrations were not consistently different from those at OO. Elevated concentrations of nitrate and depleted concentrations of DOC in the back reef lagoon relative to offshore surface waters have been documented and attributed to rapid rates of biological activity by both planktonic and benthic organisms (<xref ref-type="bibr" rid="B69">Leichter et&#xa0;al., 2013</xref>). The presence of additional sources of suspended microalgal biomass in the reef, such as released epiphytic, benthic, and coral associated microalgae, may explain the higher Chla in BR. Furthermore, the elevated concentration of silicate can be regarded as a biogeochemical marker of coastal influence to the lagoon.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Diel variation of environmental variables inside (back reef, BR; red) and outside (open ocean, OO; yellow) the coral reef. Dot plots depict the SST <bold>(A)</bold> and the concentrations of Chla <bold>(B)</bold>, nitrate <bold>(C)</bold>, nitrite <bold>(D)</bold>, ammonium <bold>(E)</bold>, phosphate <bold>(F)</bold>, silicate <bold>(G)</bold>, FDOM-T <bold>(H)</bold>, DOC <bold>(I)</bold>, DON <bold>(J)</bold>, POC <bold>(K)</bold> and PON <bold>(L)</bold>, measured over 34&#xa0;h in BR (red) and OO (yellow). Trend lines were obtained by Loess regression. Colored areas in the background depict the total solar radiation at the two sites over the sampling period. Bars on dots in <bold>(B, H, I, J)</bold> depict the standard error of duplicate analyses.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g001.tif"/>
</fig>
<p>POC was the only biogeochemical variable that showed a noticeable diel pattern at both sampling sites (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1K</bold>
</xref>). It accumulated over the day and decreased overnight at BR and OO, which may depict the diel cycle of planktonic photosynthesis (POC production) and mortality (POC loss), similar at both sites. DOC (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1J</bold>
</xref>) generally followed the opposite pattern, lower during the day and increasing during the night. This would indicate a dynamic partitioning between the two organic carbon pools over the diel cycle. At OO, FDOM-T, which is a signature of freshly produced, labile and protein-rich DOM (<xref ref-type="bibr" rid="B14">Coble, 1996</xref>), showed a clear diel pattern that paralleled that of POC, with a daytime increase, presumably from photosynthesis-driven release of DOM, and nighttime decrease, indicative of respiration-driven net consumption (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1H</bold>
</xref>). At BR, FDOM-T concentrations were higher than at OO but did not exhibit diel pattern, likely because of multiple sources besides plankton, including sediments, seaweeds, corals and groundwater discharges.</p>
</sec>
<sec id="s3_1_2">
<title>Microbial abundances</title>
<p>Heterotrophic prokaryotic abundances were very similar in BR and OO (9.1E5 &#xb1; 1.3E5 vs 8.4E5 &#xb1; 0.5E5 cells/mL; Kruskal-Wallis p&gt;0.05) and so were their diel patterns, with increased abundances in the early evening (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>). In contrast, heterotrophic prokaryotic production (as revealed by HPG incorporation) was &#x223c;3 times higher at BR compared to that at OO (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). The release of fresh and labile DOC by the coral symbionts Symbiodiniaceae and seaweeds inside the reef may trigger higher heterotrophic prokaryotic activity even at the expense of imported semi-recalcitrant DOC from the open ocean (<xref ref-type="bibr" rid="B85">Nelson et&#xa0;al., 2011</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Diel variation of microbial abundances and prokaryotic activity inside (back reef, BR; red) and outside (open ocean, OO; yellow) the coral reef. Dotplots show the abundances of heterotrophic prokaryotes <bold>(A)</bold>, the photosynthetic prokaryotes <italic>Synechococcus</italic> <bold>(C)</bold> and <italic>Prochlorococcus</italic> <bold>(D)</bold>, and photosynthetic picoeukaryotes <bold>(E)</bold> and nanoeukaryotes <bold>(F)</bold> over 36&#xa0;h at BR (red) and OO (yellow). Also shown <bold>(B)</bold> is the heterotrophic prokaryotic activity measured as L-homopropargylglycine (HPG) incorporation. Trend lines were obtained by Loess regression. Colored areas in the background depict the total solar radiation at the two sites over the sampling period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g002.tif"/>
</fig>
<p>In contrast to what was observed with heterotrophic microbes, lagoon waters (BR) harbored higher abundances of phytoplankton, especially the cyanobacterium <italic>Synechococcus</italic> and the picoeukaryotes that were, on average, 5 and 3.3 times more abundant (Kruskal-Wallis p&lt;0.01), respectively, at BR than at OO (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2C, E</bold>
</xref>). This was not significant (Kruskal-Wallis p&gt;0.05) for the nanoeukaryotic phytoplankton (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2F</bold>
</xref>) and opposite for <italic>Prochlorococcus</italic> during most of the time series (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2D</bold>
</xref>), as already documented for a nearby reef (<xref ref-type="bibr" rid="B90">Payet et&#xa0;al., 2014</xref>). Phototrophic microbes in BR did not exhibit diel synchrony; <italic>Synechococcus</italic> doubled during the day, picoeukaryotes increased by 1.5 in early night, and nanoeukaryotes increased by 1.3 in late night. <italic>Prochlorococcus</italic> appeared to follow the same diel pattern as picoeukaryotes, but the large increase on the second day may be caused by increased Chla fluorescence per cell due to much lower solar radiation, resulting in better detection in the flow cytometer (<xref ref-type="bibr" rid="B108">Sommaruga et&#xa0;al., 2005</xref>).</p>
</sec>
</sec>
<sec id="s3_2">
<title>Diel variation of the microbial community composition and diversity</title>
<p>A total of 2,018 prokaryotic and 1,473 protistan ASVs were retrieved over the diel cycles at BR and OO (<xref ref-type="supplementary-material" rid="SM1">
<bold>Figure S1A</bold>
</xref>). Rarefaction curves for both the 16S and 18S rRNA datasets and sampling time points approached a plateau in most cases, indicating that a substantial portion of microbial diversity was captured in each sample (<xref ref-type="supplementary-material" rid="SM1">
<bold>Figure S1B</bold>
</xref>). Clustering of the microbial community by their Bray-Curtis dissimilarities using the combined 16S and 18S ASV datasets revealed a clear separation of the two sampling sites (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). BR and OO shared &#x223c;25% of the total prokaryotic ASVs and &#x223c;40% of the total eukaryotic ASVs (<xref ref-type="supplementary-material" rid="SM1">
<bold>Figure S1A</bold>
</xref>). Furthermore, 70% of the prokaryotic ASVs from BR were specific to the site. In BR and OO, an average of &#x223c;57% and 37% of the prokaryotic ASVs corresponded to cyanobacterial taxa, respectively (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>). Among the cyanobacteria, the most abundant genera were <italic>Synechococcus</italic>, (80-99% predominant at BR) and <italic>Prochlorococcus</italic> (35-92% at OO), confirming the results of flow cytometry (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2</bold>
</xref>, <xref ref-type="fig" rid="f3">
<bold>3B</bold>
</xref>). The main heterotrophic prokaryotic components in BR were from the order <italic>Flavobacteriales</italic> (<italic>Bacteroidetes</italic>), representing 16-32% of the total ASVs, and the coral-reef characteristic bacteria Candidatus <italic>Actinomarina</italic> (<xref ref-type="bibr" rid="B3">Apprill et&#xa0;al., 2016</xref>), accounting for 13-22% of the prokaryotic ASVs (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). To a lesser extent, sequences of alphaproteobacterial clades (such as <italic>Rhodobacteriales</italic>, SAR11 and SAR116) and <italic>Planctomycetes</italic> (<italic>Pirellulaceae</italic>) together represented 24-40% of the total prokaryotic diversity. Essentially the same main taxonomic groups were retrieved in OO despite the low share of ASVs with BR (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). Yet, a change in the dominance was observed, with Candidatus <italic>Actinomarina</italic> being the most abundant (20-36%), followed by <italic>Flavobacteriales</italic> (19-26%), SAR11 (7-23%) and <italic>Rhodobacteriales</italic> (9-16%).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Characteristics of the microbial communities present over the diel cycles (back reef, BR) and outside (open ocean, OO) the coral reef. <bold>(A)</bold> The similarity of the microbial community structure (prokaryotes and protists together) assessed by non-metric multidimensional scaling analysis (NMDS) biplot based on Bray-Curtis dissimilarities with colored ellipses indicating the two groupings with a confidence level of 95%. <bold>(B)</bold> Diel variation of the main cyanobacterial genera in the prokaryotic assemblage at BR and OO. <bold>(C)</bold> Diel variation of the taxonomic composition of the heterotrophic prokaryotes and phototrophic eukaryotes (protists) in BR and OO. Shaded boxes in <bold>(B, C)</bold> indicate the night period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g003.tif"/>
</fig>
<p>Regarding the eukaryotes, the relative abundance and diel variation of the protistan assemblages are shown in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>. The phototrophic eukaryotic assemblages (i.e., autotrophs and mixotrophs) were similar at both sites, with abundant sequences affiliated to dinoflagellates and haptophytes (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3D</bold>
</xref>). The largest difference between the two sites was the presence of the green algae <italic>Mamiellales</italic> (specifically, <italic>Micromonas</italic> sp.) at BR, where they represented up to 53% of the eukaryotic phytoplankton sequences, and their virtual absence at OO (&lt;2.5%). Other groups present at BR and absent at OO were <italic>Cryptomonadales</italic> and diatoms.</p>
<p>The low dispersion of the data clouds in the NMDS ordination (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>) suggests that the microbial diversity was relatively stable over time at both sites, which was confirmed when examining the taxonomic compositions (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3B&#x2013;D</bold>
</xref>). In conclusion, our metabarcoding analysis confirmed the presence of two distinct bacterioplankton and phytoplankton assemblages at BR and OO, each with a rather stable composition over the diel cycle.</p>
</sec>
<sec id="s3_3">
<title>Diel variation of DMSPC concentrations inside and outside the reef</title>
<p>For the non-volatile DMSPCs (DMSP, acrylate, DMSO), there were no remarkable differences in the partitioning between the particulate and dissolved pools at the two sampling sites (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4A&#x2013;D, F, G</bold>
</xref>). DMSP was 5&#x2013;19% dissolved at BR, and 8&#x2013; 25% at OO. Acrylate was 58&#x2013;92% dissolved at BR, and 74&#x2013;95% at OO. DMSO was 88&#x2013;100% dissolved at BR, and 89-97% at OO. The particulate concentrations of the three compounds were similar at the two sites (Kruskal-Wallis p&gt;0.05), which could be coincidental or indicative of rapid connectivity through the water flow (<xref ref-type="bibr" rid="B37">Hench et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B69">Leichter et&#xa0;al., 2013</xref>). In contrast, the dissolved concentrations of DMSP and DMSO were slightly higher at OO (Kruskal-Wallis p&lt;0.05), indicative of higher microbial DMSP<sub>d</sub> consumption at BR (<xref ref-type="bibr" rid="B124">Xue et&#xa0;al., 2022</xref>) and higher photochemical DMSO<sub>d</sub> production at OO (see below). The concentrations of the volatile DMSPCs, namely DMS and DMDS, were higher at BR (Kruskal-Wallis p&lt;0.01) by factors of 1.3-3 and 1.2-&gt;20, respectively. Note that we interpret the occurrence of DMDS in the Mo&#x2019;orean seawater chromatograms as a non-quantitative reflection of the presence of methanethiol (MeSH), since the high temperatures and activated carbon of our purge and trap system are expected to partly oxidize MeSH to DMDS during the analysis (<xref ref-type="bibr" rid="B13">Cheng et&#xa0;al., 2007</xref>). Indeed, DMDS concentrations in OO (0-10 pM) were much lower than the few existing measurements of MeSH in low-Chla tropical waters of the Atlantic (100-300 pM; <xref ref-type="bibr" rid="B58">Kettle et&#xa0;al., 2001</xref>). DMS concentrations in OO (0.6-1 nM) were near the lower end of previous measurements in the tropical oligotrophic oceans (1-5 nM; <xref ref-type="bibr" rid="B15">Dani and Loreto, 2017</xref>). The higher concentrations of both compounds in BR could be due to non-planktonic sources of DMS and MeSH within the reef, such as DMSP degradation in coral holobionts (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>), seaweeds (<xref ref-type="bibr" rid="B8">Burdett et&#xa0;al., 2013</xref>), and sediments (<xref ref-type="bibr" rid="B19">Deschaseaux et&#xa0;al., 2019</xref>).</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Diel variations of particulate and dissolved DMSPC concentrations, and VOC concentrations, (back reef, BR; red) and outside (open ocean, OO; yellow) the coral reef. Dot plots show the concentrations of DMSPCs (DMSP<sub>p</sub> <bold>(A)</bold>, DMSP<sub>d</sub> <bold>(B)</bold>, acrylate<sub>t</sub> <bold>(C)</bold>, acrylate<sub>d</sub> <bold>(D)</bold>, DMS <bold>(E)</bold>, DMSO<sub>t</sub> <bold>(F)</bold>, DMSO<sub>d</sub> <bold>(G)</bold>, DMDS <bold>(J)</bold>) and VOCs (COS <bold>(H)</bold>, CS<sub>2</sub> <bold>(I)</bold>, Isoprene <bold>(K)</bold>, CH<sub>3</sub>I <bold>(L)</bold>, CH<sub>2</sub>ClI <bold>(M)</bold>, CHBr<sub>3</sub> <bold>(N)</bold>, CH<sub>2</sub>Br<sub>2</sub> <bold>(O)</bold>) over 36&#xa0;h at BR (red) and OO (yellow). Bars on dots indicate the standard error of duplicate analyses. Zero values in the DMDS and CH<sub>2</sub>ClI plots indicate below detection limit. Trend lines were obtained by Loess regression. Colored areas in the background depict the total solar radiation at the two sites over the sampling period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g004.tif"/>
</fig>
<p>Non-volatile DMSPCs exhibited diel patterns, however these patterns were different between compounds and sites. At OO, particulate DMSP (DMSP<sub>p</sub>) increased during the day and decreased at night, following solar radiation (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>). Even though DMSP<sub>p</sub> is known to be associated with phytoplankton (<xref ref-type="bibr" rid="B110">Stefels et&#xa0;al., 2007</xref> and references therein), its diel pattern did not follow size and fluorescence-based phytoplankton abundances (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>) or Chla concentrations (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). The closest pattern of a biogeochemical variable was that of POC (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1K</bold>
</xref>); however, the DMSP<sub>p</sub>/POC ratio increased during the day, somehow amplifying the diel cycle observed with POC (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). This suggests that intracellular DMSP in the open ocean varies partly with phytoplankton biomass and partly with photophysiology, so that DMSP biosynthesis increases with light (<xref ref-type="bibr" rid="B104">Sim&#xf3; et&#xa0;al., 2002</xref>). In the tropical Atlantic, <xref ref-type="bibr" rid="B4">Archer et&#xa0;al. (2018)</xref> measured higher rates (d<sup>-1</sup>) of DMSP synthesis than rates of carbon fixation into POC at all irradiances, an expected result since a substantial proportion of POC is detrital and heterotrophic biomass, while most DMSP is contained in phytoplankton. This may explain the amplitude of the DMSP<sub>p</sub>/POC ratio over the diel cycle at OO. Another example of a molecule that varies with both biomass and photophysiology is Chla, whose cellular concentration varies over diel cycles (<xref ref-type="bibr" rid="B88">Owens et&#xa0;al., 1980</xref>). At OO, Chla varied with an opposite pattern to that of POC, so that the Chla/POC ratio increased at night and decreased during the day (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>). At BR, the DMSP<sub>p</sub> diel trend was virtually opposite to that at OO, with a nighttime peak, even though the POC diel pattern was the same at both sites (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>).</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Diel variation of DMSP<sub>p</sub> and Chla concentrations normalized to the POC concentration (back reef, BR; red) and outside (open ocean, OO; yellow) the coral reef. Dotplots show the values of the DMSP<sub>p</sub>/POC <bold>(A)</bold> and Chla/POC <bold>(B)</bold> ratio over 36&#xa0;h at BR (red) and OO (yellow). Trend lines were obtained by Loess regression. Colored areas in the background depict the total solar radiation at the two sites over the sampling period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g005.tif"/>
</fig>
<p>A Spearman&#x2019;s correlation analysis (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6</bold>
</xref>) confirmed that DMSP<sub>p</sub> covaried significantly and positively with solar radiation at OO but not at BR. This discrepancy might be because, in our Mo&#x2019;orean reef lagoonal waters, DMSP<sub>p</sub> sources not only include plankton but also corals, seaweeds and sediment debris. In support of this, the 16S rRNA metabarcoding analysis (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>) revealed abundant sequences of <italic>Planctomycetes</italic> and <italic>Verrucomicrobia</italic>, typically associated with macroalgae and sediments. However, DMSP<sub>p</sub> concentrations (1.4-15.9 nM) were lower at BR over most of the diel cycle, even though Chla concentrations and phytoplankton abundances were higher, and the aforementioned contribution from debris was expected; therefore, ecophysiological explanations are to be invoked. First, the relative abundances of protistan taxonomic groups, as described by metabarcoding with the 18S rRNA gene (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>), depicted higher abundances of haptophytes and dinoflagellates at OO, especially <italic>Gymnodiniales</italic> and <italic>Prorocentrales</italic> that are reported to contain moderate to very high cellular DMSP concentrations (<xref ref-type="bibr" rid="B53">Keller et&#xa0;al., 1989</xref>) and contribute to high DMSPC concentrations in the surface ocean (<xref ref-type="bibr" rid="B100">Saint-Macary et&#xa0;al., 2023</xref>). Indeed, microscopy counts revealed that the biomasses of coccolithophores and dinoflagellates, two groups that are prolific DMSP producers, were higher at OO than at BR by a factor of 4 (Masdeu-Navarro et&#xa0;al., unpublished). Second, back reef waters contained 5 to 10-fold higher concentrations of nitrate (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1C</bold>
</xref>), likely due to microbial nitrification exacerbated by microbes associated with sediments and benthic filter-feeders (<xref ref-type="bibr" rid="B102">Scheffers et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B87">O&#x2019;Neil and Capone, 2008</xref>);. Groundwater inputs cannot be rule out either. Relieving acute nitrate limitation has been reported to decrease phytoplankton intracellular DMSP<sub>p</sub> concentrations (<xref ref-type="bibr" rid="B7">Bucciarelli and Sunda, 2003</xref>).</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Correlation matrix of the environmental variables, microbial abundances, DMSPC and VOC concentrations <bold>(A)</bold> inside (back reef, BR) and <bold>(B)</bold> outside (open ocean, OO) the coral reef over their respective diel cycles. The strength and sign of the pairwise Spearman&#x2019;s correlations (r) are shown by the color, and significance (p&lt;0.1) is indicated with a black frame. The pairwise Spearman&#x2019;s correlation of each variable to solar radiation intensity is shown by colored lines on the right side of the matrix.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-11-1341619-g006.tif"/>
</fig>
<p>DMSO<sub>p</sub> concentrations were quite low (0.1-0.6 nM) at both sites. This was unexpected, since a previous meta-analysis had shown that the intracellular DMSO pool relative to DMSP typically increases towards the high seawater temperatures observed during our study (<xref ref-type="bibr" rid="B106">Sim&#xf3; and Vila-Costa, 2006</xref>). Furthermore, DMSO<sub>p</sub> exhibited a diel peak around midnight (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4F</bold>
</xref>). The hypothesis of an antioxidant role for DMSP under high irradiances (<xref ref-type="bibr" rid="B111">Sunda et&#xa0;al., 2002</xref>) would imply higher intracellular DMSO production rates during the day, but whether this should result in intracellular accumulation is unknown. Correlation analysis (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6</bold>
</xref>) did not show covariation of DMSO<sub>p</sub> with any potentially regulatory variables, and too little is still known about this cellular component to provide a unequivocable explanation for the low levels and daily pattern of DMSO<sub>p</sub> observed in Mo&#x2019;orean waters. Particulate acrylate (acrylate<sub>p</sub>) followed diel patterns (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>) that somewhat paralleled those of DMSP<sub>p</sub> at both sites, which was expected since the latter is precursor of acrylate through intracellular cleavage (<xref ref-type="bibr" rid="B62">Kinsey and Kieber, 2016</xref>). Dissolved concentrations of DMSP (DMSP<sub>d</sub>) and acrylate (acrylate<sub>d</sub>) varied opposite to their particulate pools in OO, with a maximum at night likely attributed to intracellular release through grazing-driven mortality (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4B, D</bold>
</xref>). At BR, acrylate<sub>d</sub> and DMSO<sub>d</sub> were also opposite to their particulate pools, but DMSP<sub>d</sub> paralleled DMSP<sub>p</sub>. We note that DMSO can also be produced through cleavage of the recently-discovered intracellular component DMSOP (<xref ref-type="bibr" rid="B114">Thume et&#xa0;al., 2018</xref>), which unfortunately was not measured. A variety of microorganisms, including the microalgae haptophytes and dinoflagellates and the bacteria SAR11 and <italic>Rhodobacteriales</italic>, are capable of cleaving DMSOP to DMSO and acrylate using the same lyases for DMSP (<xref ref-type="bibr" rid="B12">Carri&#xf3;n et&#xa0;al., 2023</xref>).</p>
<p>As for the volatile DMSPCs, the most striking feature was the pronounced diel patterns of DMS and DMDS concentrations at BR (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4E, J</bold>
</xref>). Both compounds decreased at night and increased during the day, with a comparatively lesser increase on the second, cloudy day. This resulted in a significant positive correlation of DMS to solar radiation (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). This lends support to the hypothesis that DMS is produced by and released from planktonic and benthic microalgal cells (including coral-associated Symbiodiniaceae) in response to high irradiance or due to its antioxidant properties (<xref ref-type="bibr" rid="B111">Sunda et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B107">Slezak et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B25">Gal&#xed; et&#xa0;al., 2013a</xref>, <xref ref-type="bibr" rid="B27">Gal&#xed; et&#xa0;al., 2013b</xref>; <xref ref-type="bibr" rid="B67">Lawson et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>). Alternatively, the energy of midday incident radiation can easily exceed the photosynthetic electron transport capacity, conditions under which DMSP can be released, as such or upon transformation into DMS, as a strategy to dissipate excess energy (<xref ref-type="bibr" rid="B109">Stefels, 2000</xref>; <xref ref-type="bibr" rid="B63">Kinsey et&#xa0;al., 2023</xref>). The hypotheses of oxidative stress and excess energy dissipation are not mutually exclusive, and support to the latter is given by the fact that DMDS (hence MeSH) behaved the same as DMS (positive Spearman&#x2019;s correlation, <xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>), suggesting DMSP release by phytoplankton as well as corals (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>) and rapid bacterial degradation to DMS, acrylate<sub>d</sub> and MeSH. Note that the prokaryotic assemblages at the two sites (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>) contained abundant taxa within <italic>Rhodobacteriales</italic>, SAR11, SAR116 and gamma-proteobacteria that are known to harbor <italic>ddd-</italic> genes for DMSP cleavage into DMS and acrylate, as well as taxa within SAR11, <italic>Rhodobacteriales</italic>, SAR116 and other alpha-proteobacteria harboring the <italic>dmdA</italic> gene that eventually leads to MeSH production (<xref ref-type="bibr" rid="B31">Gonz&#xe1;lez et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B113">Tang and Liu, 2023</xref>). Acrylate<sub>d</sub>, in turn, would be quickly consumed by bacteria (<xref ref-type="bibr" rid="B124">Xue et&#xa0;al., 2022</xref>), and MeSH would be both biologically consumed and (photo)chemically oxidized to DMDS. In line with this, bacterial activity at BR was higher during the day (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>) and so were bacterial DMSP<sub>d</sub> and acrylate<sub>d</sub> consumption rates (<xref ref-type="bibr" rid="B124">Xue et&#xa0;al., 2022</xref>).</p>
<p>In reef lagoonal waters of the Great Barrier Reef, <xref ref-type="bibr" rid="B6">Broadbent and Jones (2006)</xref> reported diurnal increases in DMS and DMSP<sub>p</sub> concentrations, which they attributed to a physiological response of coral holobionts to increased light and temperature, including the use of these compounds by endosymbiotic Symbiodiniaceae to scavenge reactive oxygen species (<xref ref-type="bibr" rid="B51">Jones and King, 2015</xref>), and the diurnal expulsion of endosymbionts by the coral. However, short-term variation of DMSPCs was also largely affected by tides (<xref ref-type="bibr" rid="B6">Broadbent and Jones, 2006</xref>; <xref ref-type="bibr" rid="B49">Jones et&#xa0;al., 2018</xref>). Higher DMS concentrations coincided with low tides, and the greatest effect occurred when corals were exposed to air at very low tides. DMS production was further exacerbated if a low tide coincided with rainfall. The effect of tides on coral DMS production is explained by the stress that low tides impose on corals, more so if corals are exposed to air. In our Mo&#x2019;orean reef, though, conditions were very different: tides were semi-daily (low tide around 6:00 and 18:00) and weak, with an amplitude of ca. 30&#xa0;cm, and corals were not exposed to air. Our results (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4E</bold>
</xref>, <xref ref-type="fig" rid="f6">
<bold>6A</bold>
</xref>) suggest that solar radiation was the main driver of diel DMS variability in the reef.</p>
<p>The daytime increase in DMS was not observed at OO, probably because DMS was released at lower rates and concentrations were capped by DMS photolysis (<xref ref-type="bibr" rid="B26">Gal&#xed; and Sim&#xf3;, 2015</xref>). In agreement with this interpretation, the concentrations of DMSO<sub>d</sub>, a major product of DMS photooxidation (<xref ref-type="bibr" rid="B42">Hopkins et&#xa0;al., 2023</xref>), were higher at OO and sightly increased in the morning (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4G</bold>
</xref>).</p>
</sec>
<sec id="s3_4">
<title>Diel variation of VOC concentrations inside and outside the reef</title>
<sec id="s3_4_1">
<title>Other volatile sulfur compounds (COS and CS<sub>2</sub>)</title>
<p>COS concentrations ranged 5-15 pM, at the lower end of previous observations in tropical waters (3-134 pM; <xref ref-type="bibr" rid="B71">Lennartz et&#xa0;al., 2017</xref>), and were similar at the two sampling sites, only slightly higher at BR (Kruskal-Wallis p&gt;0.05; <xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4H</bold>
</xref>). COS increased in the morning, and faster at BR and on the first (sunny) day. This is consistent with COS photochemical production from the photolysis of chromophoric dissolved organic matter (<xref ref-type="bibr" rid="B116">Uher and Andreae, 1997</xref>). A positive correlation of COS to DMSO<sub>d</sub> at OO (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6</bold>
</xref>) pointed to a common origin of these two compounds through photochemical reactions in the presence of dissolved organic matter. <xref ref-type="bibr" rid="B84">Modiri Gharehveran and Shah (2018)</xref> suggested that COS may partly be formed through DMS photooxidation, like DMSO<sub>d</sub>. Note, however, that these authors used DMS concentrations as high as 14 &#xb5;M to show conversion into COS; therefore, for such a process to be a significant source of COS in marine environments (relative to UV photoproduction from dissolved organic matter), it should occur in DMS-enriched layers around cells and aggregates. In our diel study, the maximum COS concentration was followed by net consumption in the afternoon at both sampling sites (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4H</bold>
</xref>). Besides being ventilated to the atmosphere, COS is removed mainly by abiotic hydrolysis, which is accelerated in warm waters (<xref ref-type="bibr" rid="B70">Lennartz et&#xa0;al., 2020</xref>).</p>
<p>CS<sub>2</sub> concentrations varied from 25 to 75 pM, within the range of measurements in the tropical oceans (0.2-155 pM; <xref ref-type="bibr" rid="B71">Lennartz et&#xa0;al., 2017</xref>), and were higher at BR compared to OO (Kruskal-Wallis p&lt;0.05). At the sea surface, this compound is also produced photochemically from chromophoric dissolved organic matter (<xref ref-type="bibr" rid="B122">Xie et&#xa0;al., 1998</xref>) as well as biologically by phytoplankton (<xref ref-type="bibr" rid="B123">Xie et&#xa0;al., 1999</xref>). Removal processes other than ventilation to the atmosphere are unknown and thought to be inefficient (<xref ref-type="bibr" rid="B70">Lennartz et&#xa0;al., 2020</xref>), yet a first order sink process had to be invoked to fit a model to CS<sub>2</sub> observations in the Atlantic Ocean (<xref ref-type="bibr" rid="B57">Kettle, 2000</xref>). Consumption by aerobic bacteria has long been known (<xref ref-type="bibr" rid="B54">Kelly and Smith, 1990</xref>) but its relevance in seawaters has yet to be proven. As a result of the net balance between sources and sinks, CS<sub>2</sub> concentrations depicted a diel pattern at OO, with a daytime peak (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4I</bold>
</xref>). At BR, CS<sub>2</sub> concentrations were higher than in the open ocean, consistent with higher water-column integrated irradiances because of shallower mixing, and higher levels of fresh organic matter. In contrast to OO, there was no identifiable diel pattern of CS<sub>2</sub> at BR, which suggests a large contribution from a sedimentary bacterial source (<xref ref-type="bibr" rid="B61">Kim and Andreae, 1992</xref>).</p>
</sec>
<sec id="s3_4_2">
<title>Isoprene</title>
<p>Isoprene concentrations were 30-50 pM in offshore waters, within the range observed in the tropical oceans (20-90 pM; <xref ref-type="bibr" rid="B15">Dani and Loreto, 2017</xref>). Higher concentrations occurred at BR (40-120 pM) (Kruskal-Wallis p&lt;0.05; <xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4K</bold>
</xref>). A diel variation driven by sunlight was most obvious at BR, to the extent that isoprene correlated with solar radiation (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). A daytime peak for seawater isoprene has already been reported (<xref ref-type="bibr" rid="B80">Matsunaga et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B121">Wu et&#xa0;al., 2021</xref>) and suggested to be linked to phytoplankton photosynthetic activity and oxidative stress (<xref ref-type="bibr" rid="B16">Dawson et&#xa0;al., 2021</xref>). Endosymbiotic Symbiodiniaceae also produce isoprene in coral holobionts (<xref ref-type="bibr" rid="B21">Exton et&#xa0;al., 2015</xref>), especially under environmental stress (<xref ref-type="bibr" rid="B112">Swan et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B16">Dawson et&#xa0;al., 2021</xref>). Another source is the sediment microphytobenthos, which also produce more isoprene during the day (<xref ref-type="bibr" rid="B45">Hrebien et&#xa0;al., 2020</xref>). Altogether, these sources may explain the increase of isoprene concentration in the morning at BR (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4K</bold>
</xref>). Microbial and chemical (oxidation) consumption observed in these same waters (<xref ref-type="bibr" rid="B105">Sim&#xf3; et&#xa0;al., 2022</xref>) would explain the afternoon decrease. Note that major bacterial consumers of isoprene are the <italic>Actinobacteria</italic> (<xref ref-type="bibr" rid="B1">Acu&#xf1;a Alvarez et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B16">Dawson et&#xa0;al., 2021</xref>), which were abundant at both sampling sites. Additional loss by reaction with H<sub>2</sub>O<sub>2</sub> and bromoperoxidases (<xref ref-type="bibr" rid="B105">Sim&#xf3; et&#xa0;al., 2022</xref>) would have been faster at BR due to the presence of dense populations of seaweeds (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>).</p>
</sec>
<sec id="s3_4_3">
<title>Iodomethanes</title>
<p>The two iodomethanes detected and quantified were CH<sub>3</sub>I and CH<sub>2</sub>ClI. CH<sub>3</sub>I concentrations ranged 16-28 pM, at the upper end of published measurements in the tropical Pacific (0.6-19 pM; <xref ref-type="bibr" rid="B24">Fuhlbr&#xfc;gge et&#xa0;al., 2016</xref>). Concentrations were not significantly different at the two sampling sites (Kruskal-Wallis p&gt;0.05), but the diel patterns were opposite (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4L</bold>
</xref>). At OO, CH<sub>3</sub>I increased over the course of the day and decreased overnight, so that the maximum was at dusk and the minimum at dawn. Previous work suggested a photochemical source (<xref ref-type="bibr" rid="B35">Happell and Wallace, 1996</xref>; <xref ref-type="bibr" rid="B98">Richter and Wallace, 2004</xref>) that could explain this pattern. CH<sub>3</sub>I is also produced in phytoplankton cultures (diatoms, phototrophic picoeukaryotes, <italic>Prochlorococcus</italic> and <italic>Synechococcus</italic>; <xref ref-type="bibr" rid="B126">Yokouchi et&#xa0;al., 2014</xref>); furthermore, iodide methylation by both prokaryotes and eukaryotes has been seen to occur in the marine environment (<xref ref-type="bibr" rid="B2">Amachi, 2008</xref>). However, the rapid consumption overnight in the open ocean is puzzling because chemical destruction is esteemed too slow (lifetime of 8 weeks; <xref ref-type="bibr" rid="B48">Jones and Carpenter, 2007</xref>) to have a measurable, short-term impact on CH<sub>3</sub>I concentrations. At BR, CH<sub>3</sub>I concentrations decreased during the day and increased overnight, so that the maximum was at dawn and the minimum was at dusk (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4L</bold>
</xref>). This was opposite to the diel pattern observed at OO and indicates a yet unknown sunlight-dependent or circadian loss. Therefore, the role of each of the diverse reef components in CH<sub>3</sub>I cycling is yet to be resolved.</p>
<p>CH<sub>2</sub>ClI concentrations ranged between undetectable and 2 pM, at the lower end of observations in non-upwelling tropical waters (&lt;2-6 pM; <xref ref-type="bibr" rid="B50">Jones et&#xa0;al., 2010</xref>). Concentrations were comparable between sampling sites (Kruskal-Wallis p&gt;0.05), and diel patterns followed the sunlight cycle (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4M</bold>
</xref>). At BR, this was reflected by a significant positive correlation of CH<sub>2</sub>ClI to solar radiation (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). CH<sub>2</sub>ClI is mainly produced by light-enhanced halide substitution from CH<sub>2</sub>I<sub>2</sub> (<xref ref-type="bibr" rid="B77">Martino et&#xa0;al., 2006</xref>), and this is the reason why CH<sub>2</sub>I<sub>2</sub> concentrations anticorrelate with solar radiation and decrease during the day in the surface ocean (<xref ref-type="bibr" rid="B39">Hepach et&#xa0;al., 2015</xref>). CH<sub>2</sub>I<sub>2</sub> is produced by phytoplankton and especially by tropical seaweeds including the genus <italic>Turbinaria</italic> (<xref ref-type="bibr" rid="B56">Keng et&#xa0;al., 2021</xref>). Indeed, we observed CH<sub>2</sub>I<sub>2</sub> in our study, yet it was detectable only in a few samples and could not be reliably quantified.</p>
</sec>
<sec id="s3_4_4">
<title>Bromomethanes</title>
<p>Concentrations of CHBr<sub>3</sub> and CH<sub>2</sub>Br<sub>2</sub> at the open ocean site OO ranged 10-34 pM and 1-5 pM, respectively, within the lower range of previous measurements in the tropical Pacific (3-137 pM CHBr<sub>3</sub> and 2-22 pM CH<sub>2</sub>Br<sub>2</sub>; <xref ref-type="bibr" rid="B24">Fuhlbr&#xfc;gge et&#xa0;al., 2016</xref>). They showed no identifiable diel pattern (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4N, O</bold>
</xref>). Concentrations were more than an order of magnitude higher (Kruskal-Wallis p&lt;0.01) in the back reef waters of BR (289-659 pM CHBr<sub>3</sub> and 45-101 pM CH<sub>2</sub>Br<sub>2</sub>), with higher concentrations during the day, particularly on the first sunny day. This resulted in significant positive correlation of CHBr<sub>3</sub> to solar radiation (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). The two compounds were strongly positively correlated at both sites, a common feature in tropical waters (<xref ref-type="bibr" rid="B39">Hepach et&#xa0;al., 2015</xref>), with CHBr<sub>3</sub>:CH<sub>2</sub>Br<sub>2</sub> ratios around 7 (OO) and 6.5 (BR). Marine bromomethanes, especially bromoform (CHBr<sub>3</sub>), have their origin in the reaction of bromoperoxidases (BrPO) with H<sub>2</sub>O<sub>2</sub> in the presence of organic matter (<xref ref-type="bibr" rid="B74">Manley, 2002</xref>). Phytoplankton and macroalgae use BrPO to scavenge harmful levels of peroxide (<xref ref-type="bibr" rid="B10">Carpenter et&#xa0;al., 2012</xref>). Large amounts of CHBr<sub>3</sub> are produced by seaweeds in response to exposure to sunlight (<xref ref-type="bibr" rid="B55">Keng et&#xa0;al., 2013</xref>), as a mechanism to cope with oxidative stress (<xref ref-type="bibr" rid="B75">Manley and Barbero, 2001</xref>). This explains why bromomethane concentrations were so much higher at BR than at OO, given the spread of seaweed coverage across the reef crest and back reef, especially of the brown alga <italic>Turbinaria ornata</italic> (<xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>). Seaweed production also explains the strong diel cycle observed at BR, which was already reported for macroalgal-colonized coastal pools in early studies (<xref ref-type="bibr" rid="B20">Ekdahl et&#xa0;al., 1998</xref>). At OO, instead, bromomethanes were positively correlated to <italic>Synechococcus</italic>, a cyanobacterial taxon known to harbor BrPO (<xref ref-type="bibr" rid="B47">Johnson et&#xa0;al., 2011</xref>).</p>
<p>CHBr<sub>3</sub> is efficiently transformed to CH<sub>2</sub>Br<sub>2</sub> by bacteria (<xref ref-type="bibr" rid="B52">Kataoka et&#xa0;al., 2019</xref>), including <italic>Rhodobacterales</italic> (<xref ref-type="bibr" rid="B46">Ichikawa et&#xa0;al., 2015</xref>), a taxonomic group that was abundant at both sampling sites (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). Sinks for bromomethanes, besides ventilation, are photolysis (<xref ref-type="bibr" rid="B11">Carpenter and Liss, 2000</xref>), halide substitution (<xref ref-type="bibr" rid="B93">Quack and Wallace, 2003</xref>), and consumption by nitrifying bacteria (<xref ref-type="bibr" rid="B117">Wahman et&#xa0;al., 2006</xref>). Based on our dataset, we cannot say which factors controlled the dramatic consumption of bromomethanes at BR, particularly at night.</p>
</sec>
</sec>
</sec>
<sec id="s4">
<title>Summary: what controls the diel variation of DMSPC and VOC concentrations in the open ocean and in the reef lagoon?</title>
<p>Despite being in the same climatic zone, the two sampling sites were in markedly different ecosystems. The open ocean site with a water column depth of 1200&#xa0;m and the back reef lagoon with a depth of 2.5&#xa0;m, provided contrasting conditions to examine the environmental parameters and processes that controlled the diel cycles of DMSPCs and VOCs in tropical waters.</p>
<p>In the surface open ocean, vertical mixing to ca. 20&#xa0;m and low nutrient concentrations (nitrate &#x223c;0.03 &#x3bc;M) maintained low Chla concentrations (&#x223c;0.1 &#x3bc;g/L) and a phytoplankton assemblage dominated by <italic>Prochlorococcus</italic>, dinoflagellates and haptophytes. Despite higher DOC concentrations (&#x223c;73 &#x3bc;M), bacterial activity was low, probably limited by nutrient scarcity and aged carbon. In these conditions, phytoplankton DMSP represented up to 3% of total particulate organic carbon and showed a marked diel variation with strongly increasing concentrations during the day, likely due to diurnal photosynthesis and photoacclimation. In such biologically unproductive waters, photochemistry ruled most of the variation of VOCs. Indeed, the concentrations of dissolved compounds known to be photochemical products, such as DMSO, COS, CS<sub>2</sub>, CH<sub>2</sub>ClI, and potentially CH<sub>3</sub>I, increased with sunlight and decreased at night. The VOCs that have been more directly associated with open ocean phytoplankton, such as DMS, isoprene and bromomethanes, did not follow a clear diel pattern and occurred in concentrations at the lower end of previous observations in tropical waters. In these cases, low production rates were balanced by microbial, photochemical and atmospheric ventilation losses.</p>
<p>In the shallow lagoon at the back of the coral reef, the proximity of sediments, groundwater discharges, corals and abundant seaweeds resulted in higher nutrient levels (nitrate &#x223c;0.33 &#x3bc;M), higher amounts of freshly produced organic matter despite lower DOC (&#x223c;69 &#x3bc;M), higher bacterial activity, and larger microalgal populations of weaker DMSP producers like <italic>Synechococcus</italic>, <italic>Micromonas</italic> spp., diatoms and <italic>Cryptomonas</italic> spp. Consequently, DMSP and DMSO concentrations were lower but those of most VOCs were higher. A combination of photobiological and photochemical processes yielded sunny-daytime increases and nighttime decreases of DMSO, DMS, DMDS, COS, isoprene, CH<sub>2</sub>ClI and bromomethanes. Special mention is noted for the high concentrations of CS<sub>2</sub> (25-75 pM), probably contributed by sediments, and bromoform (290-660 pM) and dibromomethane (45-100 pM), largely contributed by seaweeds.</p>
<p>The interpretation of the factors governing the presence and dynamics of VOCs and DMSPCs in the two ecosystems is obviously limited by the measurements at hand. Even though we gathered a complete suite of environmental and biological variables, cause-effect links to target compound concentrations cannot be made without process studies. Having the abundances and transcripts of relevant functional genes for compound production or consumption, as well as the abundances of relevant proteins, would have been an invaluable addition to the study. Note, though, that sufficiently abundant or expressed genes have been identified for DMSPCs (<xref ref-type="bibr" rid="B72">Levine et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B31">Gonz&#xe1;lez et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B78">Masdeu-Navarro et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B113">Tang and Liu, 2023</xref>) but not for non-DMS VOCs. For the latter, the knowledge of relevant genes and enzymes is still very poor.</p>
<p>Overall, in both environments, our results highlight the importance of solar radiation in DMSPC and VOC cycling through photochemical and photobiological processes. They also send a word of caution for the design of sampling strategies to study DMSPC and VOC distributions in the surface ocean and coastal ecosystems. Attention to solar time is critical to obtain measurements that are representative of the ecosystems under study over an entire diel cycle, and to allow comparison between studies.</p>
</sec>
<sec id="s5" sec-type="data-availability">
<title>Data availability statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below:  doi: 10.5281/zenodo.10635517,  <uri xlink:href="https://www.ebi.ac.uk/ena">https://www.ebi.ac.uk/ena</uri>, PRJEB69514, <uri xlink:href="https://www.ebi.ac.uk/ena">https://www.ebi.ac.uk/ena</uri>, PRJEB69515.</p>
</sec>
<sec id="s6" sec-type="author-contributions">
<title>Author contributions</title>
<p>RS: Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Resources, Supervision, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing. MM: Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing &#x2013; original draft. JM: Data curation, Investigation, Visualization, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing. LX: Data curation, Investigation, Writing &#x2013; review &amp; editing. MC: Data curation, Investigation, Writing &#x2013; review &amp; editing. DK: Data curation, Funding acquisition, Investigation, Writing &#x2013; review &amp; editing. PR: Data curation, Investigation, Writing &#x2013; review &amp; editing. SG: Data curation, Investigation, Writing &#x2013; review &amp; editing. KB: Data curation, Investigation, Writing &#x2013; review &amp; editing. GH: Funding acquisition, Writing &#x2013; review &amp; editing. CM: Data curation, Investigation, Supervision, Writing &#x2013; review &amp; editing.</p>
</sec>
</body>
<back>
<sec id="s7" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This project has received funding from the European Research Council (ERC) under the European Union&#x2019;s Horizon 2020 research and innovation program (grant agreement #834162, SUMMIT Advanced Grant to RS). It was also funded by the Spanish Ministry of Science and Innovation (MCIN/AEI, doi: 10.13039/501100011033) through the BIOGAPS grant (CTM2016-81008-R) to RS, the &#x201c;Severo Ochoa Centre of Excellence&#x201d; accreditation (CEX2019-000298-S) to the ICM, and predoctoral grants to MM-N (BES-2017-080048) and MC-B (FPU16-01925). LX and DK were supported by funding from the National Science Foundation Chemical Oceanography program (CO-1756907) to DK. SG was supported by an Australian Government Endeavour Research Fellowship. GH received funding from the Austrian Science Fund (FWF) through project ARTEMIS (P28781-B21).</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>We thank the University of California Berkeley&#x2019;s Richard Gump Research station staff for kind hosting and logistical support during the field study. Thanks are also extended to Yaiza M. Castillo for flow cytometry re-analyses. Computing analyses from rDNA amplicon sequencing data were run at the Marine Bioinformatics Service of the ICM-CSIC (<ext-link ext-link-type="uri" xlink:href="http://marbits.icm.csic.es">http://marbits.icm.csic.es</ext-link>).</p>
</ack>
<sec id="s8" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s9" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s10" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fmars.2024.1341619/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fmars.2024.1341619/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.pdf" id="SM1" mimetype="application/pdf"/>
<supplementary-material xlink:href="Table_1.xlsx" id="SM2" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
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