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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.2025.1636874</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>High potential microbial denitrification in non-hypoxic intermediate waters of the South China Sea basin</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Zeng</surname>
<given-names>Jian</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/3076781/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Baohong</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2107789/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Shi</surname>
<given-names>Guozong</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guan</surname>
<given-names>Yanyun</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhuo</surname>
<given-names>Zesheng</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Xiamen Ocean Vocational College</institution>, <addr-line>Xiamen</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Applied Technology Engineering Center of Fujian Provincial Higher Education for Marine Resource Protection and Ecological Governance</institution>, <addr-line>Xiamen</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Xiamen Key Laboratory of Intelligent Fishery</institution>, <addr-line>Xiamen</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>Third Institute of Oceanography, Ministry of Natural Resources</institution>, <addr-line>Xiamen</addr-line>,&#xa0;<country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/927133/overview">Abhishek Srivastava</ext-link>, University of Vienna, Austria</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/1258013/overview">Wilgince Apollon</ext-link>, National Polytechnic Institute (IPN), Mexico</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/3089545/overview">Yiwen Zhou</ext-link>, Guangdong Academy of Sciences, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Jian Zeng, <email xlink:href="mailto:zengjian@xmoc.edu.cn">zengjian@xmoc.edu.cn</email>
</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>23</day>
<month>09</month>
<year>2025</year>
</pub-date>
<pub-date pub-type="collection">
<year>2025</year>
</pub-date>
<volume>12</volume>
<elocation-id>1636874</elocation-id>
<history>
<date date-type="received">
<day>28</day>
<month>05</month>
<year>2025</year>
</date>
<date date-type="accepted">
<day>01</day>
<month>09</month>
<year>2025</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2025 Zeng, Chen, Shi, Guan and Zhuo.</copyright-statement>
<copyright-year>2025</copyright-year>
<copyright-holder>Zeng, Chen, Shi, Guan and Zhuo</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>
<sec>
<title>Introduction</title>
<p>The discovery of microbial denitrification in non-extreme oxygen-deficient environments has drawn growing attention. At the same time, it is reshaping previous understanding of the spatial pattern of marine nitrogen (N) sinks. The non-hypoxic subsurface and intermediate waters of the South China Sea (SCS) basin possess potential favorable conditions for the occurrence of microbial denitrification, which are long-term overlooked and remained unexplored.</p>
</sec>
<sec>
<title>Methods</title>
<p>Methods: In this study, a series of <sup>15</sup>N-isotope tracers incubation experiments, combined with functional genes characterizations and hydro-chemical parameters analysis, were conducted during cruise. Rigorous statistical analysis was performed to reveal the correlations between environmental variables and denitrifying activity.</p>
</sec>
<sec>
<title>Results</title>
<p>It showed that representative denitrification functional genes (narG and nirS) are ubiquitously presented at moderate abundances (0.1&#xd7;10<sup>4</sup>~12&#xd7;10<sup>5</sup> copies/L) across the water columns. In the intermediate waters (600~1500 m) with low dissolved oxygen (DO) saturation (20%~30%), weak in situ denitrification rates (0.2~1.1 nmol N<sub>2</sub>/L/d) were detected. However, under simulated anoxic conditions, active denitrification was detected in most sampling layers, with potential rates (0.2~33 nmol N<sub>2</sub>/L/d) comparable to those in typical oxygen-deficient zones (ODZs).</p>
</sec>
<sec>
<title>Discussion</title>
<p>Significant correlations between suspended particulate matter (SPM) and particulate organic carbon (POC), contents with both denitrification rates and functional gene abundances were observed. It is inferred that low ambient DO levels, as well as hypoxic micro-niches in particulate matter, may together drive denitrification occurrence in the basin waters. Besides, particulate matter plays a critical role in influencing metabolic activity and spatial variability of denitrification in the basin. Since the mid-water of the SCS basin sustains a large particulate loading from terrestrial input and hydrodynamics, it is likely to maintain strong denitrification potential in the water body. We further propose a preliminary framework of coupling between particle transport driven by complex environmental dynamics and microbial N removal. Our study not only provides a potential implication for the need to re-evaluate the N budgets in the SCS basin, but also offers a new perspective of mechanism interpretation for microbial N removal in non-hypoxic marine environments.</p>
</sec>

</abstract>
<kwd-group>
<kwd>South China Sea basin</kwd>
<kwd>intermediate waters</kwd>
<kwd>potential denitrification</kwd>
<kwd>functional genes</kwd>
<kwd>low dissolved oxygen</kwd>
<kwd>particulate matters</kwd>
</kwd-group>
<counts>
<fig-count count="8"/>
<table-count count="3"/>
<equation-count count="7"/>
<ref-count count="73"/>
<page-count count="15"/>
<word-count count="8906"/>
</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">
<label>1</label>
<title>Introduction</title>
<p>The size of the fixed-N pool regulates the productivity of phytoplankton in the upper ocean, which in turn determines the ability of the marine biological pump to sequestrate atmospheric carbon dioxide (CO<sub>2</sub>) (<xref ref-type="bibr" rid="B12">Codispoti, 1989</xref>; <xref ref-type="bibr" rid="B56">Sigman and Boyle, 2000</xref>). Heterotrophic denitrification, as one of the important microbial N metabolic processes, accounts for 30~50% of inorganic fixed-N removal in modern oceans (<xref ref-type="bibr" rid="B24">Gruber, 2008</xref>; <xref ref-type="bibr" rid="B39">Lam and Kuypers, 2011</xref>; <xref ref-type="bibr" rid="B18">Devol, 2015</xref>. Traditionally, microbial N removal was recognized only occur in extreme hypoxia (dissolved oxygen (DO) concentration less than 2 &#x3bc;mol/L) (<xref ref-type="bibr" rid="B13">Codispoti et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B17">Devol, 2008</xref>; <xref ref-type="bibr" rid="B39">Lam and Kuypers, 2011</xref>). However, more and more discoveries have reported the microbial N removal, including denitrification, observed in non-hypoxic and even oxygen-replete condition across different aquatic environments (<xref ref-type="bibr" rid="B21">Fuchsman et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B66">Xia et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B51">M&#xfc;ller et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B61">Wan et&#xa0;al., 2023</xref>). The probable mechanisms were attributed to the increase of DO tolerance threshold and hypoxic micro-environment existing in the particulate matter (<xref ref-type="bibr" rid="B20">Engel et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B11">Ciccarese et&#xa0;al., 2023</xref>; <xref ref-type="bibr" rid="B14">Cram et&#xa0;al., 2024</xref>). The discovery of &#x201c;new&#x201d; N sinks implies that the spatial area of microbial N removal may be broader, and the inducing factors are more diverse than prior cognitions, which challenges the traditional concept of aquatic N sink regime. For the oceanic environment, in-depth exploration of such potential N sink is undoubtedly crucial for accurately quantifying the transformation of marine fixed-N and therefore fully characterizing the marine N cycle.</p>
<p>The South China Sea (SCS), located in the western Pacific, is the largest semi-enclosed marginal sea in the world. The extensive continental shelf and adjacent to the Pearl River estuary in the north, the Mekong River in the west and the Philippine Sea in the east, make it play a special role in global marine carbon sinks (<xref ref-type="bibr" rid="B9">Chou et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B15">Dai et&#xa0;al., 2013</xref>), and thus becoming a hotspot in the studies of biogeochemical cycles. Meanwhile, strong land-sea interactions, as well as complex hydrodynamic conditions within the basin, including mesoscale eddies and upwelling systems, have promoted the active migration and transformation of N in the SCS (<xref ref-type="bibr" rid="B68">Yang et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B67">Xu et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B60">Tian et&#xa0;al., 2025</xref>), which provides an ideal place for depicting the patterns of marginal sea N cycle. Over the past years, evidence from molecular biological identifications showed that the typical genera with anaerobic metabolism functions were widely distributed in the water column of the SCS basin, including <italic>Pseudomonas</italic> and <italic>Alcaligenes</italic> which can carry out denitrification, and <italic>Planctomyces</italic> which can carry out anaerobic ammonia oxidation (<xref ref-type="bibr" rid="B72">Zhang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B40">Li et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B46">Liu et&#xa0;al., 2021</xref>). Recently, through bacterial diversity analysis, it has also been found that several strains in the deep SCS possess the efficient denitrifying potentials (<xref ref-type="bibr" rid="B63">Wang et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B7">Chen et&#xa0;al., 2024</xref>). In addition, multi-years biogeochemical observations have confirmed that significant particulate matter inputs are common in the mid-waters of the SCS (<xref ref-type="bibr" rid="B38">Lahajnar et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B55">Schroeder et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B50">Ma et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B71">Zhang et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B58">Tan et&#xa0;al., 2020</xref>), which provides sufficient carriers for the formation of hypoxic micro-environments. Clearly, it could suppose that these potential conditions have laid a certain foundation for the occurrence of microbial denitrification in the SCS basin. However, since the SCS is a typical oligotrophic marginal sea (<xref ref-type="bibr" rid="B44">Liu et&#xa0;al., 2002</xref>) with relatively fast water exchange (<xref ref-type="bibr" rid="B23">Gong et&#xa0;al., 1992</xref>), the DO within water column would never reach extremely low level (generally higher than 70 &#x3bc;mol/L) (<xref ref-type="bibr" rid="B41">Li and Qu, 2006</xref>; <xref ref-type="bibr" rid="B43">Liu et&#xa0;al., 2011</xref>). Therefore, quantitative contribution of microbial denitrification to the N budgets of SCS basin was long been overlooked. And the inductions, spatial-temporal variations as well as modulations of denitrifying function in the SCS basin remain unknown so far.</p>
<p>In this study, a series of ship-boarded incubations by <sup>15</sup>N-isotope tracers, combined with collections and analysis of representative functional genes <italic>narG</italic>/<italic>nirS</italic> and hydro-chemical factors, were carried out during the cruise survey. The stations located in the central basin of SCS were selected to determine the original denitrification rate under simulating <italic>in-situ</italic> environment of the water body, and the potential denitrification rate under deoxygenating amended. Our study preliminarily reveals the spatial pattern and induction of denitrifying metabolism within the SCS basin. Significance of the denitrification to basin-scale N cycling is also evaluated. Additionally, a mutual coupling framework between microbial N removals and complex particle-dynamic conditions in the non-hypoxic marginal basin is tried to be constructed.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Sample collections</title>
<p>Supported by the National Natural Science Foundation of China&#x2019;s Central South China Sea Basin Scientific Expedition Research Shared Voyage (Voyage No.: KK2102-2), from July 27 to August 20, 2021, seawater samples at vertical depths of five stations in the central SCS basin were collected along the 113<sup>&#xb0;</sup>E meridian for denitrification incubating experiments and determinations of bio-chemical parameters (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). Seawaters were sampled with a Seabird SBE-911 plus conductivity-temperature-density (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>) and Rosette system. Samples for analysis of DO, dissolved inorganic nitrogen (DIN), SPM and POC were collected from surface to 1500&#xa0;m layers. Determinations of denitrification potentials and the abundance of functional genes were targeted from 300&#xa0;m to 1500&#xa0;m range (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>), the depths of which covering the typical DO minimum zones in the SCS basin (<xref ref-type="bibr" rid="B41">Li and Qu, 2006</xref>; <xref ref-type="bibr" rid="B43">Liu et&#xa0;al., 2011</xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Map of sampling stations in the SCS basin during summer 2021 cruise. In this study, the upper 1500&#xa0;m of sampling water column is divided into surface layer (0~100 m), subsurface layer (100~600 m) and intermediate layer (600~1500 m) according to previous hydrological definition.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g001.tif">
<alt-text content-type="machine-generated">Diagram illustrating sampling in the South China Sea Basin. The image shows water layers: surface (0-100m), subsurface (100-600m), and intermediate (600-1500m). Sampling includes five stations, 13 depths, six hydro-chemical parameters, two functional genes, and three incubation batches. Methods: hydrochemical analysis, metabolism incubations, and gene characterization. The map displays five sample sites marked as S-7, S-37, S-30, S-23, and S-18 with depth contours and geographic coordinates.</alt-text>
</graphic>
</fig>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Sampling strategy of bio-chemical parameters and incubation experiments through water columns of this research.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="center">Station</th>
<th valign="middle" rowspan="2" align="center">Longitude (&#xb0;E)</th>
<th valign="middle" rowspan="2" align="center">Latitude (&#xb0;N)</th>
<th valign="middle" rowspan="2" align="center">Bottom depth (m)</th>
<th valign="middle" rowspan="2" align="center">Sampling depth (m)</th>
<th valign="middle" colspan="2" align="center">Parameter sampling</th>
<th valign="middle" colspan="2" align="center">Proportion of <sup>15</sup>N in-spike (%) <sup>*</sup>
</th>
</tr>
<tr>
<th valign="middle" align="center">0~300 m</th>
<th valign="middle" align="center">300~1500 m</th>
<th valign="middle" align="center">
<italic>R<sub>in-situ</sub>
</italic> and <italic>R</italic>
<sub>potential</sub> detection</th>
<th valign="middle" align="center">Kinetics of NO<sub>3</sub>-N uptake detection <sup>&#xa7;</sup>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">S-7</td>
<td valign="middle" align="center">113.019</td>
<td valign="middle" align="center">17.011</td>
<td valign="middle" align="center">2931</td>
<td valign="top" rowspan="5" align="left">&#x2611; 5<break/>&#x2611; 25<break/>&#x2611; 50<break/>&#x2611; 75<break/>&#x2611; 100<break/>&#x2611; 150<break/>&#x2611; 300<break/>&#x2611; 500<break/>&#x2611; 600<break/>&#x2611; 700<break/>&#x2611; 800<break/>&#x2611; 1000<break/>&#x2611; 1500</td>
<td valign="top" rowspan="5" align="left">&#x2611; Temperature<break/>&#x2611; Salinity<break/>&#x2611; DO<break/>&#x2611; DIN<break/>&#x2611; SPM<break/>&#x2611; POC<break/>&#x2610; Denitrification<break/>&#x2610; <italic>narG</italic> gene<break/>&#x2610; <italic>nirS</italic> gene</td>
<td valign="top" rowspan="5" align="left">&#x2611; Temperature<break/>&#x2611; Salinity<break/>&#x2611; DO<break/>&#x2611; DIN<break/>&#x2611; SPM<break/>&#x2611; POC<break/>&#x2611; Denitrification<break/>&#x2611; <italic>narG</italic> gene<break/>&#x2611; <italic>nirS</italic> gene</td>
<td valign="top" rowspan="5" align="left">&#x2610; 0.05<break/>&#x2610; 0.10<break/>&#x2610; 0.20<break/>&#x2610; 0.40<break/>&#x2610; 0.60<break/>&#x2610; 0.80<break/>&#x2610; 1.0<break/>&#x2611; 5.0~10</td>
<td valign="top" rowspan="5" align="left">&#x2611; 0.05<break/>&#x2611; 0.10<break/>&#x2611; 0.20<break/>&#x2611; 0.40<break/>&#x2611; 0.60<break/>&#x2611; 0.80<break/>&#x2611; 1.0<break/>&#x2610; 5.0~10</td>
</tr>
<tr>
<td valign="middle" align="center">S-37</td>
<td valign="middle" align="center">112.974</td>
<td valign="middle" align="center">15.911</td>
<td valign="middle" align="center">2167</td>
</tr>
<tr>
<td valign="middle" align="center">S-30</td>
<td valign="middle" align="center">112.973</td>
<td valign="middle" align="center">13.955</td>
<td valign="middle" align="center">2560</td>
</tr>
<tr>
<td valign="middle" align="center">S-23</td>
<td valign="middle" align="center">113.019</td>
<td valign="middle" align="center">12.002</td>
<td valign="middle" align="center">4158</td>
</tr>
<tr>
<td valign="middle" align="center">S-18</td>
<td valign="middle" align="center">113.020</td>
<td valign="middle" align="center">11.023</td>
<td valign="middle" align="center">4317</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup> Proportion of <sup>15</sup>N denotes the <sup>15</sup>N-labelled fraction in bulk NO<sub>3</sub>-N substrate of incubated seawater.</p>
</fn>
<fn>
<p>
<sup>&#xa7;</sup> Kinetics of NO<sub>3</sub>-N uptake detections were only conducted in 700&#xa0;m and 1000&#xa0;m depths of Sta. S-7 and Sta. S-30.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>In order to facilitate the following discussion, the sampling water columns from surface to 1500&#xa0;m were divided into three layers in our study according to literature definition, i.e., surface waters (0~100 m), subsurface waters (100~600 m) and intermediate waters (600~1500 m) (<xref ref-type="bibr" rid="B23">Gong et&#xa0;al., 1992</xref>; <xref ref-type="bibr" rid="B41">Li and Qu, 2006</xref>; <xref ref-type="bibr" rid="B9">Chou et&#xa0;al., 2007</xref>).</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Analysis of hydro-chemical parameters</title>
<p>The collection of DO was directly transferred from rosette-sampler to a 120 mL grinding glass bottle and then sealed and stored after overflowing 3 times the volume, with the concentration being measured onboard by the standard Winkler method (<xref ref-type="bibr" rid="B26">Hansen and Koroleff, 1999</xref>). 3~5 L of seawater was filtered with a pre-combusted (450&#xb0;C, 4&#xa0;h) and weighted glass fiber membrane (Advantec GF75, 0.3 &#x3bc;m pore size). SPM and POC were collected from each sampling layer, and the filters were frozen at &#x2212;20&#xb0;C. Back to land-based laboratory, the membranes were dried and weighed at 60&#xb0;C to obtain the SPM content. After removing the inorganic carbon by fumigation with concentrated hydrochloric acid, the POC content was determined by an elemental analyzer (FlashSmart NCS, Thermo Scientific), with the detection limit of 0.1 &#x3bc;mol C of this instrument. While the filtrate of each layer seawater was collected into an acid-cleaned and sample rinsed high-density polyethylene bottle (Nalgene) and stored frozen (&#x2212;20&#xb0;C). After returning to land laboratory, the concentrations of nitrate (NO<sub>3</sub>-N) and nitrite (NO<sub>2</sub>-N) within the filtrates were determined by colorimetric method via continuous-flow Auto Analyzer III (AA3, BRAN-LUEBBE, Germany) (<xref ref-type="bibr" rid="B34">Kirkwood et&#xa0;al., 1996</xref>) (NO<sub>x</sub> was used to represent the sum of the two concentrations in this study). The detection limits for the measurement of NO<sub>2</sub>-N and NO<sub>3</sub>-N were 0.05 &#x3bc;mol/L and 0.2 &#x3bc;mol/L, respectively (hydro-chemical measurements data are available in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Data Sheet</bold>
</xref>).</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>Incubation experiments and the determination of denitrification rate</title>
<sec id="s2_3_1">
<label>2.3.1</label>
<title>Simulated incubation under <italic>in-situ</italic> conditions</title>
<p>Collection of water samples for incubation experiments was modified from <xref ref-type="bibr" rid="B5">Chang et&#xa0;al. (2014)</xref>&#x2019;s manipulation, with the samples transferred directly from rosette-bottles into pre-vacuumed 300 mL aluminum foil gas-tight sampling bags (BKMAM<sup>&#xae;</sup>), overfilled twice the volume to avoid air pollution. The microbial N removal processes (including denitrification and anammox) in water were synchronously traced using two isotopic labelling treatments, i.e., <sup>15</sup>NO<sub>3</sub>-N and <sup>15</sup>NH<sub>4</sub>-N+<sup>14</sup>NO<sub>2</sub>-N tracers, as a comparison (<xref ref-type="bibr" rid="B28">Holtappels et&#xa0;al., 2011</xref>). To maintain <italic>in situ</italic> levels of DO in water, K<sup>15</sup>NO<sub>3</sub> (&#x2265; 98.0% <sup>15</sup>N, Sigma-Aldrich) or <sup>15</sup>NH<sub>4</sub>Cl (99.0% <sup>15</sup>N, Sigma-Aldrich) + Na<sup>14</sup>NO<sub>2</sub> stock solution was added 5~10 &#x3bc;L separately into each of the two sets of aluminum foil bags via a micro-syringe following previous protocols without purging initially (<xref ref-type="bibr" rid="B30">Jensen et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B4">Bulow et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B27">Hietanen et&#xa0;al., 2012</xref>), with the final <sup>15</sup>N abundance to be 5~10% in culture system. The water samples were incubated dark in a thermostatic oscillator to simulate <italic>in-situ</italic> water body environment of each sampling layer. At 0&#xa0;h, 6&#xa0;h, 12&#xa0;h, 24&#xa0;h, and 48&#xa0;h timepoints, respectively, aliquots (10 mL) of water sample were transferred from the incubating bags to 12 mL Exetainer vials (Labco<sup>&#xae;</sup>) pre-aerated with He gas (99.999% purity), and 10 &#x3bc;L of saturated ZnCl<sub>2</sub> solution was added to stop microbial activity. The vials were sealed by 2-mm butyl rubber septa in screw caps. To avoid contact with atmosphere, all the samples were parafilm membrane sealed and refrigerated (4&#xb0;C) under water before determination (<xref ref-type="bibr" rid="B70">Zeng et&#xa0;al., 2018</xref>). All incubations were carried out in triplicates with duplicates at each timepoint.</p>
</sec>
<sec id="s2_3_2">
<label>2.3.2</label>
<title>Simulated incubation by deoxygenating amended</title>
<p>After collecting in pre-vacuumed 300 mL aluminum foil gas-tight sampling bags, the seawaters were degassed with He gas (99.999% purity) for 10~15 min prior to incubation to simulate hypoxic environment. Technically, high-pure He was introduced into the aluminum foil bag containing water sample through a polyvinyl chloride (PVC) tube connected to the valve inlet, and the background dissolved N<sub>2</sub> and O<sub>2</sub> were expelled from the valve outlet. After purging, K<sup>15</sup>NO<sub>3</sub> or <sup>15</sup>NH<sub>4</sub>Cl+Na<sup>14</sup>NO<sub>2</sub> solution (5~10 &#x3bc;L) was injected separately into two sets of sampling bags with the final <sup>15</sup>N abundance to be about 5~10%. And then, the amended seawater samples were incubated and preserved following the procedure described in Section 2.3.1 above.</p>
</sec>
<sec id="s2_3_3">
<label>2.3.3</label>
<title>Incubations of denitrifying NO<sub>3</sub>-N uptake kinetics</title>
<p>In this study, the seawaters of 700&#xa0;m and 1000&#xa0;m depths from two central basin sites (i.e., sta. S-7 and sta. S-30) were also chosen to explore the characteristics of NO<sub>3</sub>-N uptake kinetics by potential denitrification. Since the concentration of NO<sub>3</sub>-N in the SCS waters deeper than 500&#xa0;m in the SCS is generally above 20 &#x3bc;mol/L (<xref ref-type="bibr" rid="B8">Chen et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B65">Wong et&#xa0;al., 2007</xref>), which is much higher than the documented typical half-saturation constant (<italic>K</italic>
<sub>m</sub>) of denitrifying NO<sub>3</sub>-N absorption (<xref ref-type="bibr" rid="B30">Jensen et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B16">Dalsgaard et&#xa0;al., 2013</xref>), the Michaelis-Menten kinetic incubations cannot be performed directly through the NO<sub>3</sub>-N gradient setting. Therefore, a low <sup>15</sup>NO<sub>3</sub>-N in-spike experiment was used to evaluate the uptake characteristics. The principle of this method is described in Section 2.3.5. In brief of procedure, after the seawaters being collected and deoxygenated following the procedure of Section 2.3.1, low K<sup>15</sup>NO<sub>3</sub> tracer additions with <sup>15</sup>N abundance between 0.05%~1.0% were set for incubations (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) to detect the changes in the production rate of <sup>15</sup>N-labeled N<sub>2</sub> (<sup>29</sup>N<sub>2</sub>). Seawater samples were also split and preserved as Section 2.3.1.</p>
</sec>
<sec id="s2_3_4">
<label>2.3.4</label>
<title>Determinations of N<sub>2</sub> isotopic composition and denitrification rate</title>
<p>When back to the land-based laboratory, incubated seawater samples stored in vials were priorly sonicated for 40&#xa0;min at 40&#xb0;C to equilibrate N<sub>2</sub> between the headspace and solution. Compositions of <sup>15</sup>N-labeled N<sub>2</sub> species (<sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub>) in the headspace of vials were determined by a GasBench II system in combination with stable isotope ratio mass spectrometer (IRMS, DELTA<sup>Plus</sup> XP, Thermo Finnigan) (<xref ref-type="bibr" rid="B70">Zeng et&#xa0;al., 2018</xref>). The relative standard deviation of the measurement was less than 0.1%. The measured <sup>15</sup>N-N<sub>2</sub> was calibrated to eliminate background effects and the excess <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> were used to calculate the production of N<sub>2</sub> (<xref ref-type="bibr" rid="B69">Zeng et&#xa0;al., 2014</xref>). Due to the failure detection of significant <sup>29</sup>N<sub>2</sub> production in the <sup>15</sup>NH<sub>4</sub>-N+<sup>14</sup>NO<sub>2</sub>-N treatment incubations, this study disregards the potential contribution of anammox to N removal (<xref ref-type="bibr" rid="B59">Thamdrup et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B25">Hamersley et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B4">Bulow et&#xa0;al., 2010</xref>) and focuses exclusively on discussing the microbial denitrification process in the water body.</p>
<p>In <sup>15</sup>NO<sub>3</sub>-N amended incubations, the denitrification rate could be calculated as <xref ref-type="disp-formula" rid="eq1">Equation 1</xref>:</p>
<disp-formula id="eq1">
<label>(1)</label>
<mml:math display="block" id="M1">
<mml:mrow>
<mml:mi>R</mml:mi>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>30</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:msubsup>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
<mml:mn>2</mml:mn>
</mml:msubsup>
</mml:mrow>
</mml:mfrac>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>29</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:mn>2</mml:mn>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">(</mml:mo>
<mml:mn>1</mml:mn>
<mml:mo>&#x2212;</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo stretchy="false">)</mml:mo>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
</mml:mrow>
</mml:math>
</disp-formula>
<p>where <italic>R</italic>, <italic>r</italic>
<sub>29</sub> and <italic>r</italic>
<sub>30</sub> represent the production rate of total N<sub>2</sub>, <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> during incubation, respectively, and <italic>F</italic>
<sub>N</sub> is the proportion of <sup>15</sup>NO<sub>3</sub>-N in cultured system (<xref ref-type="bibr" rid="B28">Holtappels et&#xa0;al., 2011</xref>). The <italic>r</italic>
<sub>29</sub> and <italic>r</italic>
<sub>30</sub> were calculated by linear fitting of the <sup>15</sup>N-N<sub>2</sub> yielding at different incubation times. In order to eliminate the interference of <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> measurement errors on rate calculation, the final denitrification rate was obtained through arithmetic averaging as <xref ref-type="disp-formula" rid="eq2">Equation 2</xref>:</p>
<disp-formula id="eq2">
<label>(2)</label>
<mml:math display="block" id="M2">
<mml:mrow>
<mml:mi>R</mml:mi>
<mml:mo>=</mml:mo>
<mml:mo>{</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>30</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:msubsup>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
<mml:mn>2</mml:mn>
</mml:msubsup>
</mml:mrow>
</mml:mfrac>
<mml:mo>+</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>29</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:mn>2</mml:mn>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">(</mml:mo>
<mml:mn>1</mml:mn>
<mml:mo>&#x2212;</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo stretchy="false">)</mml:mo>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>}</mml:mo>
<mml:mo stretchy="false">/</mml:mo>
<mml:mn>2</mml:mn>
</mml:mrow>
</mml:math>
</disp-formula>
<p>The detection limit of the dissolved N<sub>2</sub> measurement established in this study is 0.10 nmol N<sub>2</sub>/L. Therefore, a level of 0.10 nmol N<sub>2</sub>/L/d is regarded as the minimum detection threshold for denitrification rates. That is, when the calculated rate is below this threshold, it is considered that denitrification has not occurred (incubation rate data are available in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Data Sheet</bold>
</xref>).</p>
</sec>
<sec id="s2_3_5">
<label>2.3.5</label>
<title>Characterization of NO<sub>3</sub>-N uptake kinetics</title>
<p>As described in Section 2.3.4, the relationship between denitrification rate (<italic>R</italic>) and <sup>29</sup>N<sub>2</sub> production (<italic>r</italic>
<sub>29</sub>) satisfies:</p>
<disp-formula id="eq3">
<label>(3)</label>
<mml:math display="block" id="M3">
<mml:mrow>
<mml:mi>R</mml:mi>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>29</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:mn>2</mml:mn>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">(</mml:mo>
<mml:mn>1</mml:mn>
<mml:mo>&#x2212;</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo stretchy="false">)</mml:mo>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
</mml:mrow>
</mml:math>
</disp-formula>
<p>Meanwhile, according to the Michaelis-Menten equation, there is:</p>
<disp-formula id="eq4">
<label>(4)</label>
<mml:math display="block" id="M4">
<mml:mrow>
<mml:mi>R</mml:mi>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>R</mml:mi>
<mml:mrow>
<mml:mi>m</mml:mi>
<mml:mi>a</mml:mi>
<mml:mi>x</mml:mi>
</mml:mrow>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:msub>
<mml:mi>K</mml:mi>
<mml:mi>m</mml:mi>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
</mml:mrow>
</mml:math>
</disp-formula>
<p>where <italic>R</italic>
<sub>max</sub> represents the maximum denitrifying N<sub>2</sub> production rate when NO<sub>3</sub>-N substrate supply is not limited; <italic>K</italic>
<sub>m</sub> denotes the half-saturated constant of denitrification to NO<sub>3</sub>-N absorption; [<italic>S</italic>] is the bulk NO<sub>3</sub>-N concentration within incubating system.</p>
<p>Combining <xref ref-type="disp-formula" rid="eq3">Equation 3</xref> and <xref ref-type="disp-formula" rid="eq4">4</xref> would obtain below:</p>
<disp-formula id="eq5">
<label>(5)</label>
<mml:math display="block" id="M5">
<mml:mrow>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>29</mml:mn>
</mml:mrow>
</mml:msub>
</mml:mrow>
<mml:mrow>
<mml:mn>2</mml:mn>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">(</mml:mo>
<mml:mn>1</mml:mn>
<mml:mo>&#x2212;</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo stretchy="false">)</mml:mo>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msub>
<mml:mi>R</mml:mi>
<mml:mrow>
<mml:mi>m</mml:mi>
<mml:mi>a</mml:mi>
<mml:mi>x</mml:mi>
</mml:mrow>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:msub>
<mml:mi>K</mml:mi>
<mml:mi>m</mml:mi>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
</mml:mrow>
</mml:math>
</disp-formula>
<p>Here [<italic>
<sup>14</sup>N</italic>] and [<italic>
<sup>15</sup>N</italic>] are used to denote the concentrations of <sup>14</sup>NO<sub>3</sub>-N and <sup>15</sup>NO<sub>3</sub>-N in system, respectively. Then it should deduce that under low <sup>15</sup>NO<sub>3</sub>-N tracing treatment (<italic>F</italic>
<sub>N</sub> <italic>&lt;</italic>1%), the <sup>15</sup>N proportion can be approximated by <xref ref-type="disp-formula" rid="eq6">Equation 6</xref>:</p>
<disp-formula id="eq6">
<label>(6)</label>
<mml:math display="block" id="M6">
<mml:mrow>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>15</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>&#x2248;</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>15</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>14</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mi>,</mml:mi>
<mml:mn>1</mml:mn>
<mml:mo>&#x2212;</mml:mo>
<mml:msub>
<mml:mi>F</mml:mi>
<mml:mi>N</mml:mi>
</mml:msub>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>14</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:mo stretchy="false">[</mml:mo>
<mml:mi>S</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>&#x2248;</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>14</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>14</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>=</mml:mo>
<mml:mn>1</mml:mn>
</mml:mrow>
</mml:math>
</disp-formula>
<p>and <xref ref-type="disp-formula" rid="eq5">Equation 5</xref> can be simplified as:</p>
<disp-formula id="eq7">
<label>(7)</label>
<mml:math display="block" id="M7">
<mml:mrow>
<mml:msub>
<mml:mi>r</mml:mi>
<mml:mrow>
<mml:mn>29</mml:mn>
</mml:mrow>
</mml:msub>
<mml:mo>=</mml:mo>
<mml:mfrac>
<mml:mrow>
<mml:mn>2</mml:mn>
<mml:mo>&#xd7;</mml:mo>
<mml:msub>
<mml:mi>R</mml:mi>
<mml:mrow>
<mml:mi>m</mml:mi>
<mml:mi>a</mml:mi>
<mml:mi>x</mml:mi>
</mml:mrow>
</mml:msub>
<mml:mo>&#xd7;</mml:mo>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>15</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
<mml:mrow>
<mml:msub>
<mml:mi>K</mml:mi>
<mml:mi>m</mml:mi>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>14</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:mfrac>
<mml:mo>=</mml:mo>
<mml:mi>k</mml:mi>
<mml:mo>&#xd7;</mml:mo>
<mml:msup>
<mml:mo stretchy="false">[</mml:mo>
<mml:mrow>
<mml:mn>15</mml:mn>
</mml:mrow>
</mml:msup>
<mml:mi>N</mml:mi>
<mml:mo stretchy="false">]</mml:mo>
</mml:mrow>
</mml:math>
</disp-formula>
<p>In <xref ref-type="disp-formula" rid="eq7">Equation 7</xref>, <italic>R</italic>
<sub>max</sub>, <italic>K</italic>
<sub>m</sub> and [<sup>14</sup>N] could all be regarded as constants for a specific incubation, which means that under low <sup>15</sup>NO<sub>3</sub>-N addition, the <italic>r</italic>
<sub>29</sub> against <sup>15</sup>NO<sub>3</sub>-N concentration conforms a first-order kinetic pattern. Based on the correlation, the apparent first-order kinetic coefficient (<italic>k</italic>) of potential microbial denitrification in each sampling layer can easily be quantified via linear regression between <italic>r</italic>
<sub>29</sub> against [<sup>15</sup>N] (uptake kinetics data are available in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Data Sheet</bold>
</xref>).</p>
</sec>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Molecular biological analysis of denitrifying metabolism</title>
<sec id="s2_4_1">
<label>2.4.1</label>
<title>DNA sampling and extraction</title>
<p>To characterize the typical functional genes of denitrification as well as their abundance in the SCS basin, about 4 L of seawater collected from each layer was filtered with 0.2 &#x3bc;m pore size polycarbonate membrane (Millipore, &#x424; = 47&#xa0;mm) to enrich the environmental DNA samples. The membranes were frozen in liquid N priorly and then transferred to -80&#xb0;C until further analysis. Total DNA was extracted from the particle samples in seawater with the PowerSoil DNA Isolation Kit (MO BIO Laboratories) according to the manufacturer&#x2019;s protocol. The DNA was quantified with a Qubit<sup>&#xae;</sup> 2.0 fluorometer (Life Technologies), and the quality was checked via gel electrophoresis.</p>
</sec>
<sec id="s2_4_2">
<label>2.4.2</label>
<title>Determination of functional genes abundance</title>
<p>The extracted DNA was stained with SYBR GREEN method, and the characteristic functional genes <italic>narG</italic> (encoding NO<sub>3</sub>-N reductase) and <italic>nirS</italic> (encoding NO<sub>2</sub>-N reductase) of denitrification were determined by fluorescence quantitative PCR (qPCR). The specific procedures are as follows: the PCR-amplified bands containing the target gene <italic>narG</italic> and <italic>nirS</italic> were cloned as templates, then the plasmid DNA was extracted. A 10-fold dilution was performed to establish standard curves. Fluorescence quantitative analysis of functional genes <italic>narG</italic> and <italic>nirS</italic> were conducted using the extracted total DNA as a template. The primer pairs for <italic>narG</italic> were narG-1960m2f/narG-2050m2r (<xref ref-type="bibr" rid="B37">L&#xf3;pezguti&#xe9;rrez et&#xa0;al., 2004</xref>) and for <italic>nirS</italic> were Cd3aF/R3cd (<xref ref-type="bibr" rid="B29">Jarvis et&#xa0;al., 2004</xref>). The PCR amplification protocol included: denaturation (95&#xb0;C/5&#xa0;min), annealing (95&#xb0;C/15 s), extension (60&#xb0;C/30 s), and 40 cycles. The PCR reaction system (40 &#x3bc;L of total volume) comprised 20 &#x3bc;L of mixture A (18 &#x3bc;L of 2&#xd7;SYBR real-time PCR premixture and 1 &#x3bc;L each of forward and reverse primers), 10 &#x3bc;L of diluted DNA template, and 10 &#x3bc;L of sterile distilled water. Sterilized seawater was taken as the negative control, and each sample was analyzed in triplicate. Quantitative analysis exhibited a reliable performance. For gene <italic>narG</italic>, the amplification efficiency of was 98.5%, with a standard curve R<sup>2</sup> of 0.999 and a detection limit of 50 copies/mL. For gene <italic>nirS</italic>, the amplification efficiency of was 99.8%, with a standard curve R<sup>2</sup> of 0.998 and a detection limit of 10 copies/mL (analytic raw data of functional genes are available in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Data Sheet</bold>
</xref>).</p>
</sec>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>Statistical analysis</title>
<p>The stations mapping, statistical analysis, and data visualization were performed using ODV 7.5, SPSS 26.0, and Origin 10.0 software, respectively. In this study, the Shapiro-Wilk test was applied to assess the normality of experimental data, while Levene&#x2019;s test was used to evaluate the homogeneity of variances. The significant differences between simulated incubation groups, the spatial distribution of environmental factors and the correlation coefficients of regressions were all tested via one-way ANOVA. When either test indicated a violation of the ANOVA assumptions (<italic>p</italic> &lt; 0.05), significance was evaluated using the Kruskal-Wallis test, followed by the Wilcoxon test for <italic>post-hoc</italic> comparisons. Independence of observations was guaranteed by the randomized block design and confirmed by plotting residuals against predicted values; no discernible patterns or temporal autocorrelation were detected. Outliers with studentized residuals &gt; 3 were examined and retained only when measurement errors could be ruled out. A significant threshold of <italic>p</italic> &lt; 0.05 was used in all analyses. Correlations between variables were determined using Principal Component Analysis (PCA), Redundancy Analysis (RDA), and Spearman&#x2019;s rank correlation analysis. To account for multiple comparisons, false discovery rate (FDR) adjustment was applied using the Benjamini-Hochberg procedure to all pairwise correlation tests, with an FDR-adjusted <italic>q</italic>-value threshold of 0.05 considered statistically significant.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<sec id="s3_1">
<label>3.1</label>
<title>Spatial distributions of DO and NO<sub>x</sub>
</title>
<p>The DO profiles of five sampling stations showed a consistent vertical pattern (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2B, C</bold>
</xref>). In the surface waters, there was a sharp DO decline to 120~130 &#x3bc;mol/L with a saturation of about 50%. In the subsurface waters, DO concentrations and saturations continued to decrease with depth but gradually. The typical DO minimum occurred in intermediate waters at 700~800 m, with the lowest DO concentrations among stations ranging between 78.8~90.6 &#x3bc;mol/L and the saturation at 25.3~28.7% level. Below this depth, DO exhibited a gradual increasing trend. The vertical DO pattern observed in our cruise was consistent with the previous reports (<xref ref-type="bibr" rid="B23">Gong et&#xa0;al., 1992</xref>; <xref ref-type="bibr" rid="B41">Li and Qu, 2006</xref>; <xref ref-type="bibr" rid="B43">Liu et&#xa0;al., 2011</xref>). Horizontally, both DO concentrations and saturations displayed an overall increasing trend from north to south among five stations.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Distributions of hydro-chemical parameters across sampling stations. <bold>(A)</bold> <italic>&#x3b8;</italic>-S diagram throughout the upper 1500&#xa0;m depth; <bold>(B)</bold> Profiles of dissolved oxygen; <bold>(C)</bold> Profiles of dissolved oxygen saturation; <bold>(D)</bold> Profiles of total NO<sub>3</sub>-N + NO<sub>2</sub>-N in waters; <bold>(E)</bold> Profiles of suspended particulate matter; <bold>(F)</bold> Profiles of particulate organic matter; <bold>(G)</bold> Profiles of organic fraction in particulate matter.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g002.tif">
<alt-text content-type="machine-generated">Seven panels present oceanographic data. Panel A shows potential temperature versus salinity with colored data points. Panels B to G depict various measurements: dissolved oxygen (DO) in micromoles per liter, DO saturation percentage, NOx in micromoles per liter, suspended particulate matter (SPM) in milligrams per liter, particulate organic carbon (POC) in micromoles per liter, and fractional POC (fPOC) percentage, all plotted against depth in meters, with different colored lines representing stations S-7, S-37, S-30, S-23, and S-18. Colors in panel A correlate with depth on a vertical gradient scale.</alt-text>
</graphic>
</fig>
<p>The NO<sub>x</sub> concentrations increased with depth, ranging from 0.00 to 13.83 &#x3bc;mol/L in surface water and 8.98 to 24.93 &#x3bc;mol/L in subsurface water, both showing a spatial variance of higher in the north and lower in the south. While in the intermediate layers, NO<sub>x</sub> varied between 21.97 and 31.25 &#x3bc;mol/L with less variation across depths, and no significant differences were observed among sampling stations (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2D</bold>
</xref>) (ANOVA test, <italic>p</italic> &gt; 0.05).</p>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Spatial patterns of SPM and POC</title>
<p>During the sampling period, the SPM content across all stations ranged from 0.10 to 0.86 mg/L, with a pulse increase in each water layer (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2E</bold>
</xref>). An obvious SPM peak in the surface layer appeared at 75~100 m depths, with a content between 0.41~0.79 mg/L. In subsurface layer, a slight increase was observed at 500~600 m, with the content between 0.28~0.69 mg/L. In the intermediate layer, the peak appeared at depths of 800~1000 m, showing a larger variation among stations (0.22~0.87 mg/L). The POC concentrations in water column ranged from 0.08 to 1.17 &#x3bc;mol C/L. Vertically, all stations showed higher POC in surface waters and lower contents in subsurface and middle layers (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2F, G</bold>
</xref>). Although less pronounced than SPM, slightly elevated POC were still observed at depths of 500~600 m and 700~800 m across stations. The increased loading both of SPM and POC in the&#xa0;subsurface and intermediate waters implies potential contributions from external inputs within these two layers. Horizontally, both SPM and POC concentrations among stations generally exhibited a decreasing trend from north to south.</p>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Denitrification rate in the water column</title>
<p>To ensure the reliability of denitrification rate measurements and exclude possible misinterpretation caused by detecting bias, data validation was conducted based on formula (1) in Section 2.3.4. If N<sub>2</sub> only derived from microbial denitrification in the incubation system, the metabolism rates (<italic>R</italic>) calculated from <italic>r</italic>
<sub>29</sub> and <italic>r</italic>
<sub>30</sub> should be coincident. Regression analysis revealed that the N<sub>2</sub> production rates calculated from <italic>r</italic>
<sub>29</sub> and <italic>r</italic>
<sub>30</sub> of all incubations followed a 1:1 linear relationship (R<sup>2</sup>&#xa0;=&#xa0;0.997, <italic>p</italic> &lt; 0.001) (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). This confirms that the detected <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> in the incubation system were exclusively derived from denitrifying yield (<xref ref-type="bibr" rid="B25">Hamersley et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B28">Holtappels et&#xa0;al., 2011</xref>).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Data validation and spatial pattern of incubated denitrification rates across sampling stations. <bold>(A)</bold> Linear relationship between <sup>29</sup>N<sub>2</sub> production (<italic>r</italic>
<sub>29</sub>) and <sup>30</sup>N<sub>2</sub> production (<italic>r</italic>
<sub>30</sub>) considering all incubations during the cruise; <bold>(B, C)</bold> Vertical distributions of denitrification rates under ambient DO levels (<italic>R<sub>in-situ</sub>
</italic>) and deoxygenated conditions (<italic>R</italic>
<sub>potential</sub>) throughout the sampling water column; <bold>(D)</bold> Comparison of average denitrification rates variation among different stations. Gray areas in <bold>(B, C)</bold> represent the intermediate water layer.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g003.tif">
<alt-text content-type="machine-generated">A set of four scientific charts illustrate various datasets. Chart A is a scatter plot showing a strong positive correlation between \( r_{29} \) and \( r_{30} \) derived \( N_2 \) production, with a slope of 0.997. Charts B and C display line graphs of \( R_{in-situ} \) and \( R_{potential} \) over different depths, with multiple colored lines representing different stations. Chart D is a bar graph comparing average \( R_{in-situ} \) and \( R_{potential} \) across five stations, using blue and red bars, respectively. Error bars are present in all charts for variability depiction.</alt-text>
</graphic>
</fig>
<p>Under <italic>in-situ</italic> DO condition of the seawaters, the N<sub>2</sub> production above detection limit only accounted for 28.6% of all incubations. The detected rates (referred to as <italic>R<sub>in-situ</sub>
</italic> hereafter) ranged from 0.20&#xa0;&#xb1;&#xa0;0.08 to 1.07&#xa0;&#xb1;&#xa0;0.23 nmol N<sub>2</sub>/L/d (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>), and all the N<sub>2</sub> productions observed were confined in the intermediate layer (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>). Among stations, the average <italic>R<sub>in-situ</sub>
</italic> within 600~1500 m depths differed significantly (ANOVA test, <italic>p</italic> &lt; 0.05), exhibiting a decreasing trend from north to south (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3D</bold>
</xref>). The highest mean <italic>R<sub>in-situ</sub>
</italic> was observed at Sta. S-7 (0.41&#xa0;&#xb1;&#xa0;0.13 nmol N<sub>2</sub>/L/d), while the lowest level occurred at Sta. S-23 (0.03&#xa0;&#xb1;&#xa0;0.01 nmol N<sub>2</sub>/L/d).</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Measurements of denitrification rate in the SCS basin under ambient DO levels and deoxygenated conditions.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="3" align="center">Depth(m)</th>
<th valign="middle" colspan="10" align="center">Incubated denitrification rates (nmol N<sub>2</sub>/L/d)</th>
</tr>
<tr>
<th valign="middle" colspan="2" align="center">S-7</th>
<th valign="middle" colspan="2" align="center">S-37</th>
<th valign="middle" colspan="2" align="center">S-30</th>
<th valign="middle" colspan="2" align="center">S-23</th>
<th valign="middle" colspan="2" align="center">S-18</th>
</tr>
<tr>
<th valign="middle" align="center">
<italic>R</italic>
<sub>in-situ</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>potental</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>in-situ</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>potential</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>in-situ</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>potential</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>in-situ</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>potential</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>in-situ</sub>
</th>
<th valign="middle" align="center">
<italic>R</italic>
<sub>potential</sub>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">300</td>
<td valign="middle" align="center">n.d <sup>*</sup>
</td>
<td valign="middle" align="center">0.27&#xa0;&#xb1;&#xa0;0.08</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
</tr>
<tr>
<td valign="middle" align="center">500</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">6.86&#xa0;&#xb1;&#xa0;3.22</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">1.75&#xa0;&#xb1;&#xa0;0.61</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
</tr>
<tr>
<td valign="middle" align="center">600</td>
<td valign="middle" align="center">0.31&#xa0;&#xb1;&#xa0;0.15</td>
<td valign="middle" align="center">1.59&#xa0;&#xb1;&#xa0;0.78</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">2.82&#xa0;&#xb1;&#xa0;1.04</td>
<td valign="middle" align="center">0.25&#xa0;&#xb1;&#xa0;0.11</td>
<td valign="middle" align="center">2.87&#xa0;&#xb1;&#xa0;1.21</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">0.16&#xa0;&#xb1;&#xa0;0.05</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
</tr>
<tr>
<td valign="middle" align="center">700</td>
<td valign="middle" align="center">1.07&#xa0;&#xb1;&#xa0;0.23</td>
<td valign="middle" align="center">32.8&#xa0;&#xb1;&#xa0;11.8</td>
<td valign="middle" align="center">0.55&#xa0;&#xb1;&#xa0;0.17</td>
<td valign="middle" align="center">25.8&#xa0;&#xb1;&#xa0;8.26</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">10.2&#xa0;&#xb1;&#xa0;4.98</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">4.29&#xa0;&#xb1;&#xa0;1.76</td>
<td valign="middle" align="center">0.27&#xa0;&#xb1;&#xa0;0.11</td>
<td valign="middle" align="center">10.5&#xa0;&#xb1;&#xa0;4.74</td>
</tr>
<tr>
<td valign="middle" align="center">800</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">21.4&#xa0;&#xb1;&#xa0;6.85</td>
<td valign="middle" align="center">0.40&#xa0;&#xb1;&#xa0;0.14</td>
<td valign="middle" align="center">27.3&#xa0;&#xb1;&#xa0;12.8</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">3.59&#xa0;&#xb1;&#xa0;1.72</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">1.57&#xa0;&#xb1;&#xa0;0.72</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">3.18&#xa0;&#xb1;&#xa0;1.46</td>
</tr>
<tr>
<td valign="middle" align="center">1000</td>
<td valign="middle" align="center">0.65&#xa0;&#xb1;&#xa0;0.26</td>
<td valign="middle" align="center">26.3&#xa0;&#xb1;&#xa0;13.2</td>
<td valign="middle" align="center">0.20&#xa0;&#xb1;&#xa0;0.08</td>
<td valign="middle" align="center">5.43&#xa0;&#xb1;&#xa0;2.50</td>
<td valign="middle" align="center">0.65&#xa0;&#xb1;&#xa0;0.23</td>
<td valign="middle" align="center">5.26&#xa0;&#xb1;&#xa0;2.31</td>
<td valign="middle" align="center">0.21&#xa0;&#xb1;&#xa0;0.09</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
</tr>
<tr>
<td valign="middle" align="center">1500</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">5.53&#xa0;&#xb1;&#xa0;1.82</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">1.02&#xa0;&#xb1;&#xa0;0.32</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">0.26&#xa0;&#xb1;&#xa0;0.13</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
<td valign="middle" align="center">n.d</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>n.d denotes the measurement below detection limit.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>In contrast, significant N<sub>2</sub> production under deoxygenating amended was much more pervasively observed, accounting for 65.7% of incubations. The measured potential denitrification rates (referred to as <italic>R</italic>
<sub>potential</sub> hereafter) ranged from 0.16&#xa0;&#xb1;&#xa0;0.07 to 32.8&#xa0;&#xb1;&#xa0;11.2 nmol N<sub>2</sub>/L/d, higher by 1~2 orders of magnitude than <italic>R<sub>in-situ</sub>
</italic> (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>). Except for the 300&#xa0;m and 500&#xa0;m at Sta. S-7 and Sta. S-37, detected potential denitrification all occurred in the intermediate waters (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). Notably, much higher <italic>R</italic>
<sub>potential</sub> compared to other sampling depths was observed at 700&#xa0;m and 800&#xa0;m across all stations, suggesting some favorable conditions for denitrification performance within these two water layers. Similar to the spatial pattern of <italic>R<sub>in-situ</sub>
</italic>, the <italic>R</italic>
<sub>potential</sub> showed a marked horizontal variability by decreasing from north to south also (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3D</bold>
</xref>). The mean <italic>R</italic>
<sub>potential</sub> across 600~1500 m depths was highest at Sta. S-7 (17.5&#xa0;&#xb1;&#xa0;6.7 nmol N<sub>2</sub>/L/d) and lowest at Sta. S-23 (1.20&#xa0;&#xb1;&#xa0;0.51 nmol N<sub>2</sub>/L/d). It implies that specific mechanisms within the basin may sustain microbial denitrification potential.</p>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Abundances of functional genes <italic>narG</italic> and <italic>nirS</italic>
</title>
<p>As key functional genes involved in microbial denitrification, both <italic>narG</italic> and <italic>nirS</italic> genes were detected through the 300~1500 m depths during our cruise (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4A, B</bold>
</xref>), which provided a biological basis for the prevalent denitrifying potential observed in the SCS waters. The abundance of <italic>narG</italic> and <italic>nirS</italic> ranged from 0.55&#xd7;10<sup>5</sup> to 12.5&#xd7;10<sup>5</sup> copies/L and 0.14&#xd7;10<sup>4</sup> to 5.51&#xd7;10<sup>4</sup> copies/L, respectively. There is a significant linear correlation between these two genes (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>), suggesting a synergistic operation of nitrate reduction (<italic>narG</italic>-mediated) and nitrite reduction (<italic>nirS</italic>-mediated) in shaping denitrification potential of the basin waters, while nitrate reduction likely plays a dominant role. Vertically, both the genes exhibited depth-dependent variations, with peak abundances focused on 700~1000 m depths across stations (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4A, B</bold>
</xref>). Horizontally, there was also a notable north-south gradient, with Sta. S-7 and Sta. S-37 bearing higher abundance compared to the other three stations (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4D</bold>
</xref>). The spatial distributions of these two functional genes further indicate probable differences in the community structure of denitrifying microorganisms across the study area.</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Spatial pattern of functional genes <italic>narG</italic> and <italic>nirS</italic> across sampling stations. <bold>(A, B)</bold> Vertical distributions of <italic>narG</italic> and <italic>nirS</italic> genes abundances within 300~1500 m depths; <bold>(C)</bold> Correlation analysis between <italic>narG</italic> and <italic>nirS</italic> abundances; <bold>(D)</bold> Variation of average two functional genes abundance among different stations.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g004.tif">
<alt-text content-type="machine-generated">Graphs illustrate the distribution and abundance of narG and nirS genes at various depths and locations. Graph A shows narG gene copies per liter with depth, while Graph B displays nirS data similarly. Graph C highlights the correlation between narG and nirS abundances with a line of best fit, R squared value of 0.82, and p-value of 0.00008. Graph D compares average abundances of narG (blue) and nirS (red) genes across locations S-7, S-37, S-30, S-23, and S-18.</alt-text>
</graphic>
</fig>
</sec>
<sec id="s3_5">
<label>3.5</label>
<title>Kinetics of NO<sub>3</sub>-N uptake by potential denitrification</title>
<p>Characterization of NO<sub>3</sub>-N uptake kinetic experiments revealed a linear increase of <sup>29</sup>N<sub>2</sub> production rates (<italic>r</italic>
<sub>29</sub>) against the corresponding K<sup>15</sup>NO<sub>3</sub> in-spike gradients at each targeted sampling depth (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5</bold>
</xref>). According to formula (7) in Section 2.3.5, the apparent first-order kinetic coefficients (<italic>k</italic>) of denitrifying metabolism for 700&#xa0;m and 1000&#xa0;m at Sta. S-7 and Sta. S-30 were calculated (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). The <italic>k</italic> values at both depths in Sta. S-7 were significantly higher than those at Sta. S-30, indicating spatial variability in the NO<sub>3</sub>-N utilization capacity of denitrifying microorganisms. If the measured <italic>R</italic>
<sub>potential</sub> in each depth is considered as the NO<sub>3</sub>-N saturated denitrification rate [i.e., <italic>R</italic>
<sub>max</sub> in formula (7)], then the corresponding half-saturated constants (<italic>K</italic>
<sub>m</sub>) are derived (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). In contrast to the coefficient <italic>k</italic>, the <italic>K</italic>
<sub>m</sub> values varied non-significant (<italic>p</italic> &gt; 0.05) among four depths, with an average of 2.41&#xa0;&#xb1;&#xa0;0.19 &#x3bc;mol/L, which suggests a consistent affinity of potential denitrifying metabolism to NO<sub>3</sub>-N substrate in the basin waters.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Denitrifying NO<sub>3</sub>-N uptake characterization with low <sup>15</sup>NO<sub>3</sub>-N gradient in-spike modulating <sup>29</sup>N<sub>2</sub> production.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g005.tif">
<alt-text content-type="machine-generated">Graph illustrating the relationship between \(^{15}\text{NO}_3\text{-N}\) concentration and \(^{29}\text{N}_2\) production rate. Four linear lines represent different conditions: S-7 at 700m (blue), S-7 at 1000m (green), S-30 at 700m (pink), and S-30 at 1000m (brown). Slopes are given as \(k_1 = 0.057\), \(k_2 = 0.044\), \(k_3 = 0.019\), \(k_4 = 0.009\) nmol/L/d, showing higher rates for deeper depths and lower slopes for shallower ones. Error bars indicate variability.</alt-text>
</graphic>
</fig>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Calculations of kinetic constants of denitrifying NO<sub>3</sub>-N uptake across the basin waters.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center">Station</th>
<th valign="middle" align="center">Depth (m)</th>
<th valign="middle" align="center">Apparent first-order kinetic coefficient <italic>k</italic> (d<sup>-1</sup>)</th>
<th valign="middle" align="center">Half-saturated constant <italic>K<sub>m</sub>
</italic>(&#x3bc;mol/L)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" rowspan="2" align="center">S-7</td>
<td valign="middle" align="center">700</td>
<td valign="middle" align="center">0.057&#xa0;&#xb1;&#xa0;0.002</td>
<td valign="middle" align="center">2.32&#xa0;&#xb1;&#xa0;0.13</td>
</tr>
<tr>
<td valign="middle" align="center">1000</td>
<td valign="middle" align="center">0.044&#xa0;&#xb1;&#xa0;0.002</td>
<td valign="middle" align="center">2.38&#xa0;&#xb1;&#xa0;0.15</td>
</tr>
<tr>
<td valign="middle" rowspan="2" align="center">S-30</td>
<td valign="middle" align="center">700</td>
<td valign="middle" align="center">0.019&#xa0;&#xb1;&#xa0;0.001</td>
<td valign="middle" align="center">2.25&#xa0;&#xb1;&#xa0;0.09</td>
</tr>
<tr>
<td valign="middle" align="center">1000</td>
<td valign="middle" align="center">0.009&#xa0;&#xb1;&#xa0;0.001</td>
<td valign="middle" align="center">2.68&#xa0;&#xb1;&#xa0;0.21</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<sec id="s4_1">
<label>4.1</label>
<title>Induction of microbial denitrification in the SCS basin waters</title>
<p>During sampling period, detectable microbial denitrifying was pervasively observed in the subsurface and intermediate waters across the SCS basin, which have rarely been reported in previous studies. Although the <italic>R<sub>in-situ</sub>
</italic> incubated under ambient DO was relatively weak and the gene abundances were much lower, the denitrification potential rates <italic>R</italic>
<sub>potential</sub> of the basin could reach a high level comparable to those measurements in oxygen-deficient waters (8~200 nmol/L/d; <xref ref-type="bibr" rid="B30">Jensen et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B16">Dalsgaard et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B5">Chang et&#xa0;al., 2014</xref>). Since lack of hypoxic condition in the water column, denitrifying metabolism was considered as negligible (<xref ref-type="bibr" rid="B44">Liu et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B68">Yang et&#xa0;al., 2017</xref>). That means unrecognized mechanisms remain to be revealed regarding the fixed-N removal within the basin. To better elucidate the inducing factors of observed potential denitrification, statistical analyses are conducted on the distributions and correlations among hydro-chemical parameters, incubation rates, and functional genes. PCA analysis reveals that the environmental factors and denitrification functions in the intermediate waters of northern stations (Sta. S-7 and Sta. S-37) significantly differed from other layers, characterized by low DO, high SPM loading, elevated denitrification rates and high functional gene abundances (<xref ref-type="fig" rid="f6">
<bold>Figures&#xa0;6A, B</bold>
</xref>). RDA and Spearman analyses further indicate marked negative correlations of denitrification rate and gene abundance against DO and its saturation, while denitrification rate correlates positively with both SPM and POC contents (<xref ref-type="fig" rid="f6">
<bold>Figures&#xa0;6C, D</bold>
</xref>). These findings highlight the dominant roles of DO and particulate matter in inducing the activity of denitrifying metabolism in the SCS basin waters.</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Statistical analysis of hydro-chemical and metabolic factors. <bold>(A, B)</bold> PCA analysis of environmental and metabolic factors across 300~1500 m depths, respectively; <bold>(C)</bold> RDA analysis of microbial metabolism and environmental factors; <bold>(D)</bold> Spearman correlation matrix of hydro-chemical factors, functional genes and metabolic rates (numerical label in diagram denotes the Spearman coefficient; <sup>*</sup>
<italic>p</italic> &lt; 0.05, <sup>**</sup>
<italic>p</italic> &lt; 0.01). POC/SPM and <italic>narG</italic>/<italic>nirS</italic> in the figure represent the mass fraction of organic carbon in SPM and abundance ratio of two genes, respectively (Spearman correlations data are available in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Data Sheet</bold>
</xref>).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g006.tif">
<alt-text content-type="machine-generated">Four-panel figure depicting statistical analyses and correlations. Panel A shows a PCA biplot with two principal components, colored markers for different samples, and environmental factors. Panel B is another PCA biplot with similar elements. Panel C presents an RDA biplot with variables and arrows indicating directions. Panel D shows a heatmap of Spearman correlations among variables with a color gradient from blue to red.</alt-text>
</graphic>
</fig>
<p>Traditionally, microbial denitrification, as an anaerobic metabolic process, was believed to occur only under strictly hypoxic conditions (DO &lt; 2 &#x3bc;mol/L) (<xref ref-type="bibr" rid="B13">Codispoti et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B17">Devol, 2008</xref>). Therefore, coastal hypoxic waters, pelagic ODZs and marine sediments have been well documented as primary regions for denitrification performance (<xref ref-type="bibr" rid="B39">Lam and Kuypers, 2011</xref>; <xref ref-type="bibr" rid="B18">Devol, 2015</xref>). However, the ambient DO level at subsurface and intermediate waters of the basin during cruise ranged between 80~120 &#x3bc;mol/L, far above typical hypoxic threshold. And even historical minimum DO records were as high as 65~75 &#x3bc;mol/L (<xref ref-type="bibr" rid="B43">Liu et&#xa0;al., 2011</xref>). Then there comes a query, that is whether the <italic>R<sub>in-situ</sub>
</italic> detected in this study resulted from oxygen depletion by microbial respiration in the incubation period? In previous report, the heterotrophic bacteria in the intermediate SCS waters were counted at about 2&#xd7;10<sup>6</sup> cells/L (<xref ref-type="bibr" rid="B42">Li et&#xa0;al., 2015</xref>). Adopting the representative microbial respiratory rate of 0.3 fmol O<sub>2</sub>/cell/d (<xref ref-type="bibr" rid="B54">Robinson, 2008</xref>), a simple arithmetic suggests that bacterial oxygen consumption over the 48-hours incubation would only be &lt; 0.1 &#x3bc;mol/L, which is negligible compared to the ambient DO contents. And in fact, we also selected the 800&#xa0;m and 1000&#xa0;m of Sta. S-7 and measured the remaining DO concentrations within aluminum foil bags to be about 68 &#x3bc;mol/L after incubations. This reckoning thus rules out experimental interference from bacterial respiration and indicates the adaptation of denitrification to the oxygenated water environments. Actually, not a few denitrifying bacteria in nature exhibit facultative anaerobic metabolism, capable of tolerating a broad range of DO levels (<xref ref-type="bibr" rid="B73">Zumft, 1997</xref>). Earlier laboratory experiments have demonstrated that strains such as <italic>Pseudomonas nautica</italic>, <italic>Pseudomonas stutzeri</italic>, and <italic>Paracoccus denitrificans</italic> could turn to express denitrifying function when DO saturations below 70% (<xref ref-type="bibr" rid="B3">Bonin et&#xa0;al., 1989</xref>; <xref ref-type="bibr" rid="B36">K&#xf6;rner and Zumft, 1989</xref>). Based on incubations of coastal Namibia and Peru hypoxic waters, <xref ref-type="bibr" rid="B32">Kalvelage et&#xa0;al. (2011)</xref> revealed that nitrate reductase activity (mediating the NO<sub>3</sub>-N &#x2192; NO<sub>2</sub>-N step in denitrification) persisted even at about 30 &#x3bc;mol/L oxygen level. In addition, some research also confirmed that in fluctuating redox environments (e.g., tidal zone) the DO tolerance threshold of denitrification could elevate to about 90 &#x3bc;mol/L (<xref ref-type="bibr" rid="B22">Gao et&#xa0;al., 2010</xref>). Intriguingly, N-cycling genera, including <italic>Halomonas</italic>, <italic>Idiomarina</italic> and <italic>Pseudoalteromonas</italic>, which have been identified with high denitrification efficiency and aerobic denitrifying potential, were recently isolated from the deep SCS basin (<xref ref-type="bibr" rid="B63">Wang et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B7">Chen et&#xa0;al., 2024</xref>). These findings provide critical biological evidence supporting the observed denitrification activity within the basin waters.</p>
<p>Apart from the adaptation of denitrifying bacteria to O<sub>2</sub> tolerance, SPM in the water column is also one of the important ways to induce denitrification in non-hypoxic environments. Because of its large specific surface area and organic-rich composition, SPM is beneficial for the attachment and growth of aquatic microorganisms (<xref ref-type="bibr" rid="B72">Zhang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B2">Bianchi et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B1">Balmonte et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B61">Wan et&#xa0;al., 2023</xref>). It is easy to generate hypoxic structures inside particles with severe aerobic respiration, thus creating ideal micro-niches for anaerobic metabolism by bacteria such as denitrification (<xref ref-type="bibr" rid="B53">Ploug, 2001</xref>; <xref ref-type="bibr" rid="B66">Xia et&#xa0;al., 2021</xref>). This phenomenon has been widely documented. For instance, laboratory simulations demonstrated active denitrification within organic polymer aggregates secreted from phytoplankton even under ambient DO levels higher than 100 &#x3bc;mol/L (<xref ref-type="bibr" rid="B35">Klawonn et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B57">Stief et&#xa0;al., 2016</xref>). <xref ref-type="bibr" rid="B21">Fuchsman et&#xa0;al. (2019)</xref> reported that spring phytoplankton blooms in the Black Sea basin triggered vigorous denitrification within the oxygenated subsurface layer (DO in the range of 30~50 &#x3bc;mol/L) due to elevated SPM inputs. Similarly, in the well-oxygenated Beibu Gulf, <xref ref-type="bibr" rid="B70">Zeng et&#xa0;al. (2018)</xref> observed pronounced denitrification in the bottom nepheloid layers driven by sediment resuspension. The detected high denitrification potential in our study consistently coincided with elevated SPM loads in sampling depths, which means SPM, as a carrier, might also play a pivotal role in activating denitrification metabolism within the SCS waters.</p>
<p>Obviously, both DO and SPM act as critical factors in inducing denitrifying function of the SCS seawaters. Regarding the incubation measurements, the Spearman correlations and significance levels of these two factors against <italic>R<sub>in-situ</sub>
</italic> as well as <italic>R</italic>
<sub>potential</sub> showed no marked difference (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>), remaining it still difficult to discern the dominance between DO and SPM. While in terms of functional genes, DO exhibited a more significant correlation compared to SPM (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>). Furthermore, both <italic>narG</italic> and <italic>nirS</italic> abundances positively correlated with <italic>R<sub>in-situ</sub>
</italic> and <italic>R</italic>
<sub>potential</sub> strongly (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>). Based on the above analyses, it could be speculated that low DO level likely prior induces the functional genes expression associated with anaerobic denitrifying metabolism in the basin waters. Then SPM further triggers enzymatic activity by providing available metabolic niches, and ultimately performs high denitrification potential. Since there was no pronounced correlation of <italic>narG</italic>/<italic>nirS</italic> ratio against either DO or SPM according to Spearman analysis (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>), the response of denitrifying functional structure to these two environmental factors remains unclear and deeper explorations are still necessary.</p>
</sec>
<sec id="s4_2">
<label>4.2</label>
<title>Relationship between SPM and potential denitrification in the basin waters</title>
<p>SPM not only provides favorable micro-environments for microbial N removal under non-hypoxic conditions, but also contributes the carbon source for heterotrophic metabolisms such as denitrification. Therefore, SPM serves as an important link for coupling micro-scale carbon and nitrogen cycles in aquatic ecosystems (<xref ref-type="bibr" rid="B2">Bianchi et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B61">Wan et&#xa0;al., 2023</xref>). In order to further elucidate the influence of SPM content and its composition on the denitrification function of the SCS basin, the intermediate water body (600~1500 m) with prominent potential denitrifying activity is focused for discussion below.</p>
<p>Linear and exponential fitting regressions were applied to analyze relationships of SPM and POC against to <italic>R<sub>in-situ</sub>
</italic>, <italic>R</italic>
<sub>potential</sub>, <italic>narG</italic> and <italic>nirS</italic> gene abundances, respectively (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7</bold>
</xref>). The results showed that increased SPM and POC levels significantly enhanced functional genes expression and denitrification potential, consistent with observations across diverse aquatic systems, including rivers, estuaries, coastal zones, and pelagic oceans (<xref ref-type="bibr" rid="B70">Zeng et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B21">Fuchsman et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B1">Balmonte et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B66">Xia et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B61">Wan et&#xa0;al., 2023</xref>). It reflects a common modulatory role of particulate matter on denitrification and implies that particle-associated denitrifying bacteria may contribute more substantially to denitrification potential than their free-living counterparts within the basin waters (<xref ref-type="bibr" rid="B31">Jia et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B72">Zhang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B70">Zeng et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B40">Li et&#xa0;al., 2021</xref>). Comparing the regressions among several scenarios, it is found that, on the one hand, both SPM and POC fit better with <italic>R</italic>
<sub>potential</sub> and <italic>nirS</italic> abundance than fittings with <italic>R<sub>in-situ</sub>
</italic> and <italic>narG</italic> abundance (ANOVA test, <italic>p</italic> &lt; 0.01). Since the interface of particles usually promotes the metabolic activity of microorganisms (<xref ref-type="bibr" rid="B42">Li et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B35">Klawonn et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B1">Balmonte et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B61">Wan et&#xa0;al., 2023</xref>), denitrification potential will exhibit stronger dependence on particulate matter and organic carbon under deoxygenated conditions. It suggests that when O<sub>2</sub>-inhibition relieved, the particulate matters will play a dominant role in modulating spatial pattern of denitrifying process. Thermodynamically, the Gibbs free energy of <italic>narG</italic>-mediated NO<sub>3</sub>-N to NO<sub>2</sub>-N reduction (&#x25b3;<italic>G</italic>
<sup>0</sup> = -244 kJ) is greater than that of <italic>nirS</italic>-mediated NO<sub>2</sub>-N to NO reduction (&#x25b3;<italic>G</italic>
<sup>0</sup> = -371 kJ) (<xref ref-type="bibr" rid="B39">Lam and Kuypers, 2011</xref>), which means a more electron donor (carbon source) demand of the latter step and thus explains the observed disparities in gene-specific regressions. On the other hand, exponential fittings in the regression analyses generally show superior goodness compared to linear ones (ANOVA test, <italic>p</italic> &lt; 0.05), indicating complex nonlinear relationships between particulate matter and denitrification potential as well as functional genes expression. Notably, the influence of particulate matter on the denitrifying function is not solely mediated by its abundance. Previous studies have emphasized that particle size, compositional heterogeneity and organic carbon source collectively influence microbial denitrification activity on particles (<xref ref-type="bibr" rid="B35">Klawonn et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B31">Jia et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B70">Zeng et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B21">Fuchsman et&#xa0;al., 2019</xref>).</p>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>Regression fittings between microbial, metabolic factors and particulate matter content with <bold>(A&#x2013;E)</bold> regarding SPM, <bold>(F&#x2013;J)</bold> regarding POC. Blue and black lines in graph are regressions based on linear fitting, while red line is based on exponential fitting.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g007.tif">
<alt-text content-type="machine-generated">Graphs show relationships between variables such as SPM, POC, and kinetic coefficients. Each subplot (A-J) presents data points, error bars, and trend lines with correlation coefficients (R) and p-values. SPM-related graphs (A-E) and POC-related graphs (F-J) highlight trends in nmol/L/day, natG, nirS abundance, and kinetic coefficients, offering statistical insights with varying R values and significance levels.</alt-text>
</graphic>
</fig>
<p>Worth mentioning, the high particulate loading observed in the intermediate waters during cruise was not an accident. According to former estimations, up to 7&#xd7;10<sup>10</sup> tons of terrigenous sediments annually from Luzon island in the east, mountainous rivers of Taiwan in the northeast, Pearl river runoff in the north, Red river in the northwest, Mekong river in the southwest as well as Malay Peninsula in the south, can be imported into the SCS basin (<xref ref-type="bibr" rid="B47">Liu et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B55">Schroeder et&#xa0;al., 2015</xref>). Driven by mid-depth circulation, these terrestrial materials are transported and dispersed for a long distance across the basin, resulting in widespread high particulate export features in the middle and deep of SCS waters (<xref ref-type="bibr" rid="B47">Liu et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B55">Schroeder et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B64">Wei et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B50">Ma et&#xa0;al., 2017</xref>). Moreover, during the summer southwest monsoon, intensified upwelling systems in the SCS (<xref ref-type="bibr" rid="B6">Chao et&#xa0;al., 1996</xref>; <xref ref-type="bibr" rid="B44">Liu et&#xa0;al., 2002</xref>) would enhance sediment resuspensions over the shelf and stimulate primary productivity in upper layers (<xref ref-type="bibr" rid="B19">Dippner et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B45">Liu et&#xa0;al., 2007</xref>). Concurrently, hydrological dynamics such as mesoscale eddies and typhoon events further amplify the vertical and lateral transport of SPM and POC into the deep basin (<xref ref-type="bibr" rid="B62">Wang et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B33">Kao et&#xa0;al., 2010</xref>). Sediment trap data also corroborated that summer SPM fluxes in the intermediate waters (1000~2000 m) increase prominently, accompanied by 1~2 fold elevations in POC input and organic matter degradability (<xref ref-type="bibr" rid="B38">Lahajnar et&#xa0;al., 2007</xref>). It can be inferred that favorable hydrodynamic conditions which sustain particulate and organic matters supply, likely contribute to maintaining the strong denitrification potential in the intermediate of SCS basin.</p>
<p>By comparison, it is found that the spatial trend of <italic>R</italic>
<sub>potential</sub> as well as average functional genes abundances observed in our cruise is in good agreement with the pattern of sinking particle plumes, which were depicted by <xref ref-type="bibr" rid="B55">Schroeder et&#xa0;al. (2015)</xref> covering the whole SCS basin (<xref ref-type="fig" rid="f8">
<bold>Figure&#xa0;8A</bold>
</xref>). Synthesizing the above discussions, a preliminary conceptual framework of coupling between denitrification and SPM in the SCS basin is then proposed, as schematically described in <xref ref-type="fig" rid="f8">
<bold>Figure&#xa0;8B</bold>
</xref>. That is, the particulate matters from terrestrial or benthic sediments are priorly imported and dispersed across the basin-wide seawater driven by hydrodynamics, accompanied by the attachment of plentiful microorganisms. When transported to the intermediate waters, low ambient DO stimulates the expression of anaerobic denitrifying function and also facilitates hypoxic micro-niches creation in particles. Finally, the bacterial denitrifying metabolism is fueled with sufficient organic carbon supply. Although needing to be confirmed, the coupling framework provides a novel perspective for unraveling the mechanisms driving microbial N removal in non-hypoxic marginal basins.</p>
<fig id="f8" position="float">
<label>Figure&#xa0;8</label>
<caption>
<p>A schematic illustration of the occurrence of potential denitrification process in the non-hypoxic SCS basin waters. <bold>(a)</bold> A general spatial matching of observed denitrifying function during our cruise with documented particulate matter transport and load patterns across the basin from <xref ref-type="bibr" rid="B55">Schroeder et&#xa0;al. (2015)</xref>&#x2019;s development; <bold>(b)</bold> A conceptual framework of coupling between microbial N removals and complex particle dynamics in the non-hypoxic marginal basin.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmars-12-1636874-g008.tif">
<alt-text content-type="machine-generated">Diagram depicting oceanographic data and processes. Panel (a) shows depth profile with data on R potential integration, narG abundance, nirS abundance, typical dissolved oxygen profile, and suspended particulate matter transports across various latitudes. Panel (b) illustrates coastal and offshore oceanic processes, including runoff inputs, nearshore and offshore upwelling, mesoscale eddies, and deep circulations. The inset highlights microbial denitrification in the South China Sea Basin.</alt-text>
</graphic>
</fig>
<p>To further assess the importance of this particle-loaded N removal to nutrient cycling in the SCS, we compare measured denitrification with major microbial N-transformations of the basin. When integrating <italic>R<sub>in-situ</sub>
</italic> and <italic>R</italic>
<sub>potential</sub> throughout the intermediate water column (600~1500 m) among five sampling stations, average fluxes of 175.1 &#x3bc;mol N/m<sup>2</sup>/d and 6.39 mmol N/m<sup>2</sup>/d are obtained, respectively. The depth-integrated <italic>R<sub>in-situ</sub>
</italic> is comparable to the import flux from N<sub>2</sub> fixation in SCS upper euphotic zone, while the depth-integrated <italic>R</italic>
<sub>potential</sub> is 1~2 orders of magnitude higher (<xref ref-type="bibr" rid="B49">Lu et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B48">Liu et&#xa0;al., 2023</xref>; <xref ref-type="bibr" rid="B60">Tian et&#xa0;al., 2025</xref>). Besides, both <italic>R<sub>in-situ</sub>
</italic> and <italic>R</italic>
<sub>potential</sub> detected in our incubation assays are within the range of reported nitrification rates in SCS subsurface layer (0.1~100 nmol/L/d; <xref ref-type="bibr" rid="B67">Xu et&#xa0;al., 2018</xref>). It implies that the microbial denitrifying function discovered should be ecologically meaningful, which might have a basin-scale impact on NO<sub>3</sub>-N budget balance and nutrient cycling patterns of SCS. Given our study relying on only a single cruise, basin-wide investigations covering seasonal and interannual variations remain extremely limited. How the potential denitrification would affect primary productivity in the upper SCS is still unknown, requiring more robust observations and model verification in future research.</p>
</sec>
<sec id="s4_3">
<label>4.3</label>
<title>Variability of substrate NO<sub>3</sub>-N uptake in seawaters</title>
<p>The <italic>K</italic>
<sub>m</sub> constant (2.25~2.68 &#x3bc;mol/L) of potential denitrification in this study estimated via <sup>15</sup>NO<sub>3</sub>-N gradient incubation is well consistent with literature reports. For example, laboratory-isolated strains such as <italic>Paracoccus denitrificans</italic>, <italic>Pseudomonas chlororaphis</italic>, and <italic>Pseudomonas aureofaciens</italic> exhibited <italic>K</italic>
<sub>m</sub> values of 5.0 &#x3bc;mol/L, 1.7 &#x3bc;mol/L and 1.8 &#x3bc;mol/L, respectively (<xref ref-type="bibr" rid="B52">Parsonage et&#xa0;al., 1985</xref>; <xref ref-type="bibr" rid="B10">Christensen and Tiedje, 1988</xref>). Similarly, <xref ref-type="bibr" rid="B30">Jensen et&#xa0;al. (2009)</xref> reported a <italic>K</italic>
<sub>m</sub> of 2.9 &#x3bc;mol/L for denitrification in the hypoxic Denmark Mariager Fjord. While <xref ref-type="bibr" rid="B16">Dalsgaard et&#xa0;al. (2013)</xref> measured a value of 2.5 &#x3bc;mol/L in the oxygen-deficient Gotland Basin of Baltic Sea. This result indirectly reflects the potential denitrification observed in the SCS to be typical anaerobic denitrifying metabolism, with nitrate reductase exhibiting strong substrate affinity for NO<sub>3</sub>-N. Comparing with the NO<sub>3</sub>-N concentration in the intermediate waters (20~29 &#x3bc;mol/L), it further confirms that substrate availability is sufficient for denitrification performance. This is also consistent with the insignificant correlation between incubated denitrification rates and NO<sub>3</sub>-N concentration (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>).</p>
<p>Different from the constant <italic>K</italic>
<sub>m</sub>, the apparent first-order kinetic coefficient <italic>k</italic> varied markedly among sampling layers (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). Additionally, there appears strong linear correlations of <italic>k</italic> with both SPM and POC contents in corresponding layers (<xref ref-type="fig" rid="f7">
<bold>Figures&#xa0;7E, J</bold>
</xref>). As mentioned in the methods, coefficient <italic>k</italic> in our discussion reflects the apparent activity of nitrate reductase. Although it could not rule out the contribution of change in denitrifying bacterial community composition to the variation of enzymatic activity (<xref ref-type="bibr" rid="B42">Li et&#xa0;al., 2015</xref>, <xref ref-type="bibr" rid="B40">Li et&#xa0;al., 2021</xref>), the correlations between <italic>k</italic> and SPM as well as POC verified a dominant role of particulate matter content in mediating the potential denitrification in our study region. Indeed, the &#x201c;interfacial effect&#x201d; between particle-water interface favors substrate diffusion and migration more effectively, thereby stimulating higher metabolic activity for particle-attached bacteria compared to those free-living ones (<xref ref-type="bibr" rid="B47">Liu et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B72">Zhang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B40">Li et&#xa0;al., 2021</xref>).</p>
</sec>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusions</title>
<p>Our study provides the empirical evidence of microbial denitrification occurrence in the intermediate waters of the SCS basin at moderately low DO level (80~100 &#x3bc;mol/L), with incubated potential rates under deoxygenated condition comparable to those measurements documented in typical ODZs. It indicates that the denitrification potential inner SCS basin has been long underestimated. Combined with statistical analyses, it is inferred a synergistic mechanism wherein bacteria adapting to ambient DO levels as well as hypoxic micro-environments provided by particulate matter jointly might induce the activation of denitrification metabolism. Significant correlations were robustly verified with SPM and POC in seawaters against denitrification rates (including <italic>R<sub>in-situ</sub>
</italic> and <italic>R</italic>
<sub>potential</sub>), functional gene abundances (<italic>narG</italic> and <italic>nirS</italic>) and kinetic coefficient (<italic>k</italic>), which underscores the dominant roles of particulate matter and organic carbon in modulating enzymatic activity, N removal potential and spatial variability of denitrification in the SCS basin. Supported by multi-year biogeochemical observations, it is hypothesized that the persistent high particle-loading in the intermediate waters might importantly contribute to sustaining the basin-wide denitrification potential and probably have significant impact on nutrient cycling of the SCS basin. Based on these insights, we further propose a preliminary conceptual framework coupling complex particulate dynamics with microbial N removal processes in typical marginal basins, which offers a novel perspective for re-evaluating potential N sinks in non-hypoxic marine environments.</p>
</sec>
</body>
<back>
<sec id="s6" sec-type="data-availability">
<title>Data availability statement</title>
<p>The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author contributions</title>
<p>JZ: Writing &#x2013; original draft, Conceptualization, Writing &#x2013; review &amp; editing. BC: Conceptualization, Supervision, Writing &#x2013; review &amp; editing. GS: Investigation, Data curation, Methodology, Writing &#x2013; original draft. YG: Validation, Writing &#x2013; review &amp; editing, Formal analysis, Methodology. ZZ: Formal analysis, Investigation, Writing &#x2013; review &amp; editing.</p>
</sec>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research and/or publication of this article. This work was supported by the Nature Science Foundation of Fujian Province (2022J05071), Educational Research Project for Young and Middle-aged Teachers of Fujian Province (Science and Technology Category) (JAT210802) and Xiamen Key Laboratory of Intelligent Fishery (XMKLIF-ZR-202407).</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>We thank the captain and crew of the R/V Tan Kan Kee for their assistance in sampling.</p>
</ack>
<sec id="s9" 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="s10" sec-type="ai-statement">
<title>Generative AI statement</title>
<p>The author(s) declare that no Generative AI was used in the creation of this manuscript.</p>
<p>Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.</p>
</sec>
<sec id="s11" 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="s12" 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.2025.1636874/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fmars.2025.1636874/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Table1.xlsx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
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