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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id>
<journal-title>Frontiers in Microbiology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Microbiol.</abbrev-journal-title>
<issn pub-type="epub">1664-302X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fmicb.2022.845321</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Microbiology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Selenite Reduction by <italic>Proteus</italic> sp. YS02: New Insights Revealed by Comparative Transcriptomics and Antibacterial Effectiveness of the Biogenic Se<sup>0</sup> Nanoparticles</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author"><name><surname>Wang</surname><given-names>Yuting</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
<xref rid="fn0004" ref-type="author-notes"><sup>&#x2020;</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ye</surname><given-names>Qing</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
<xref rid="fn0004" ref-type="author-notes"><sup>&#x2020;</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1655255/overview"/>
</contrib>
<contrib contrib-type="author"><name><surname>Sun</surname><given-names>Yujun</given-names></name>
<xref rid="aff3" ref-type="aff"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Yulu</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Meng</surname><given-names>Bo</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Du</surname><given-names>Jun</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname><given-names>Jingjing</given-names></name>
<xref rid="aff1" ref-type="aff"><sup>1</sup></xref>
<xref rid="aff2" ref-type="aff"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tugarova</surname><given-names>Anna V.</given-names></name>
<xref rid="aff4" ref-type="aff"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Kamnev</surname><given-names>Alexander A.</given-names></name>
<xref rid="aff4" ref-type="aff"><sup>4</sup></xref>
<xref rid="c001" ref-type="corresp"><sup>&#x002A;</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1619740/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Huang</surname><given-names>Shengwei</given-names></name>
<xref rid="aff3" ref-type="aff"><sup>3</sup></xref>
<xref rid="c001" ref-type="corresp"><sup>&#x002A;</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1369452/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China</institution>, <addr-line>Hefei</addr-line>, <country>China</country></aff>
<aff id="aff2"><sup>2</sup><institution>Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China</institution>, <addr-line>Hefei</addr-line>, <country>China</country></aff>
<aff id="aff3"><sup>3</sup><institution>Institute of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University</institution>, <addr-line>Fengyang</addr-line>, <country>China</country></aff>
<aff id="aff4"><sup>4</sup><institution>Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms&#x2014;Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences</institution>, <addr-line>Saratov</addr-line>, <country>Russia</country></aff>
<author-notes>
<fn id="fn0001" fn-type="edited-by">
<p>Edited by: Qiaoyun Huang, Huazhong Agricultural University, China</p>
</fn>
<fn id="fn0002" fn-type="edited-by">
<p>Reviewed by: Judith Maria Braganca, Birla Institute of Technology and Science, India; Monica Sharma, Babasaheb Bhimrao Ambedkar University, India</p>
</fn>
<corresp id="c001">&#x002A;Correspondence: Alexander A. Kamnev, <email>aakamnev@ibppm.ru</email>; <email>a.a.kamnev@mail.ru</email>; Shengwei Huang, <email>swhuang@ipp.ac.cn</email>
</corresp>
<fn id="fn0003" fn-type="other">
<p>This article was submitted to Microbiotechnology, a section of the journal Frontiers in Microbiology</p>
</fn>
<fn id="fn0004" fn-type="equal">
<p><sup>&#x2020;</sup>These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>10</day>
<month>03</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>845321</elocation-id>
<history>
<date date-type="received">
<day>29</day>
<month>12</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>17</day>
<month>02</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2022 Wang, Ye, Sun, Jiang, Meng, Du, Chen, Tugarova, Kamnev and Huang.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Wang, Ye, Sun, Jiang, Meng, Du, Chen, Tugarova, Kamnev and Huang</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Biotransformation of selenite by microorganisms is an effective detoxification (in cases of dissimilatory reduction, e.g., to Se<sup>0</sup>) and assimilation process (when Se is assimilated by cells). However, the current knowledge of the molecular mechanism of selenite reduction remains limited. In this study, a selenite-resistant bacterium was isolated and identified as <italic>Proteus</italic> sp. YS02. Strain YS02 reduced 93.2% of 5.0&#x2009;mM selenite to selenium nanoparticles (SeNPs) within 24&#x2009;h, and the produced SeNPs were spherical and localized intracellularly or extracellularly, with an average dimension of 140&#x2009;&#x00B1;&#x2009;43&#x2009;nm. The morphology and composition of the isolated and purified SeNPs were characterized using dynamic light scattering (DLS), scanning electron microscopy (SEM) with energy-dispersive X-ray (EDX) spectrometry, and Fourier transform infrared (FTIR) spectroscopy. FTIR spectroscopy indicated the presence of proteins, polysaccharides, and lipids on the surface of the isolated SeNPs. Furthermore, the SeNPs showed excellent antimicrobial activity against several Gram-positive and Gram-negative pathogenic bacteria. Comparative transcriptome analysis was performed to elucidate the selenite reduction mechanism and biosynthesis of SeNPs. It is revealed that 197 genes were significantly upregulated, and 276 genes were significantly downregulated under selenite treatment. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that genes associated with ABC transporters, sulfur metabolism, pentose phosphate pathway (PPP), and pyruvate dehydrogenase were significantly enhanced, indicating selenite is reduced by sulfite reductase with PPP and pyruvate dehydrogenase supplying reducing equivalents and energy. This work suggests numerous genes are involved in the response to selenite stress, providing new insights into the molecular mechanisms of selenite bioreduction with the formation of SeNPs.</p>
</abstract>
<kwd-group>
<kwd><italic>Proteus</italic> sp. YS02</kwd>
<kwd>selenite biotransformation</kwd>
<kwd>biogenic selenium nanoparticles</kwd>
<kwd>transcriptome</kwd>
<kwd>antibacterial effectiveness</kwd>
</kwd-group>
<contract-num rid="cn1">2108085QC88</contract-num>
<contract-num rid="cn1">2008085MC60</contract-num>
<contract-num rid="cn2">KJ2021A0881</contract-num>
<contract-num rid="cn3">121032300311-5</contract-num>
<contract-sponsor id="cn1">Natural Science Foundation of Anhui Province<named-content content-type="fundref-id">10.13039/501100003995</named-content></contract-sponsor>
<contract-sponsor id="cn2">Anhui Provincial Department of Education</contract-sponsor>
<contract-sponsor id="cn3">Russian Academy of Sciences<named-content content-type="fundref-id">10.13039/501100002674</named-content></contract-sponsor>
<counts>
<fig-count count="11"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="51"/>
<page-count count="13"/>
<word-count count="8204"/>
</counts>
</article-meta>
</front>
<body>
<sec id="sec1" sec-type="intro">
<title>Introduction</title>
<p>Selenium (Se) is a metalloid that plays a vital role in maintaining human health (<xref ref-type="bibr" rid="ref3">Chen et al., 2021</xref>). It can replace sulfur in cysteine and be co-translationally incorporated as selenocysteine (SeCys) in selenoproteins involved in biological processes, including detoxification, anti-inflammation, antioxidant defense, and thyroid functioning. A trace amount of selenium is important for human health. Selenium deficiency in humans has been associated with cardiovascular disease, thyroid dysfunction, and immune system dysfunction (<xref ref-type="bibr" rid="ref30">Pedrero et al., 2006</xref>). Selenium supplementation can protect animals and ameliorate the toxic effects of heavy metals (<xref ref-type="bibr" rid="ref8">Ge et al., 2021</xref>), improve the clinical symptoms of heart failure (<xref ref-type="bibr" rid="ref2">Al-Mubarak et al., 2021</xref>), stimulate the immune response toward cancer cells (<xref ref-type="bibr" rid="ref47">Yazdi et al., 2012</xref>), and alleviate oxidative stress-induced intestinal epithelial barrier injury (<xref ref-type="bibr" rid="ref31">Song et al., 2017a</xref>). However, selenium is also known as a &#x201C;double-edged sword&#x201D; element&#x2014;it is essential to human and animal health in trace amounts but is toxic in excess (<xref ref-type="bibr" rid="ref27">Nancharaiah and Lens, 2015b</xref>). Moreover, the toxicity of selenium is not merely defined by its concentration but is also dependent on its speciation. In nature, selenium exists in different forms, including selenite (SeO<sub>3</sub><sup>2&#x2212;</sup>), selenate (SeO<sub>4</sub><sup>2&#x2212;</sup>), selenide (Se<sup>2&#x2212;</sup>), and as an elementary substance (Se<sup>0</sup>). Among these, selenite is the most toxic form for aquatic life and humans because of its high mobility in aqueous environments and high bioavailability. However, elemental selenium is biologically inert and generally thought to be non-toxic (<xref ref-type="bibr" rid="ref31">Song et al., 2017a</xref>). Furthermore, compared with selenium, nanosized elemental selenium particles possess much higher bioactivity and biosafety properties, including improved antioxidant, anticancer functions, and antibacterial activity. Therefore, selenium nanoparticles (SeNPs) may be a more valuable selenium-adding form and therapeutic agent for human health and are attracting increasing attention.</p>
<p>Microorganisms are crucial in the global biogeochemical cycle of selenium on the Earth&#x2019;s surface. Microbial transformation of selenite and selenate can occur both aerobically or anaerobically. More importantly, selenite/selenate transformation is often accompanied by the formation of SeNPs existing either inside the cytoplasm, within the periplasm, or extracellularly (<xref ref-type="bibr" rid="ref29">Ojeda et al., 2020</xref>). Se<sup>0</sup> particles formed by Se-oxyanion reducing microorganisms, including <italic>Azospirillum thiophilum</italic> (<xref ref-type="bibr" rid="ref38">Tugarova et al., 2018</xref>), <italic>Azospirillum brasilense</italic> (<xref ref-type="bibr" rid="ref15">Kamnev et al., 2017</xref>, <xref ref-type="bibr" rid="ref14">2021</xref>), yeast (<xref ref-type="bibr" rid="ref19">Kieliszek et al., 2015</xref>, <xref ref-type="bibr" rid="ref20">2016</xref>; <xref ref-type="bibr" rid="ref13">Jim&#x00E9;nez-Lamana et al., 2018</xref>), <italic>Enterobacter cloacae</italic> Z0206 (<xref ref-type="bibr" rid="ref31">Song et al., 2017a</xref>), <italic>Stenotrophomonas maltophilia</italic> SeITE02 (<xref ref-type="bibr" rid="ref24">Lampis et al., 2017</xref>), <italic>Bacillus</italic> sp. Y3 (<xref ref-type="bibr" rid="ref46">Yasir et al., 2020</xref>), <italic>Comamonas testosteroni</italic> S44 (<xref ref-type="bibr" rid="ref34">Tan et al., 2018</xref>), etc., have been reported. So far, it has been found that bacterial Se(IV) reduction may occur through enzymatic or nonenzymatic mechanisms (<xref ref-type="bibr" rid="ref37">Tugarova and Kamnev, 2017</xref>). Specifically, the non-enzymatic reduction of selenite is mediated by biogenic glutathione, iron siderophores, and sulfide (<xref ref-type="bibr" rid="ref26">Nancharaiah and Lens, 2015a</xref>). For enzyme-dependent reduction, reductases encompassing sulfite reductase (<xref ref-type="bibr" rid="ref11">Huang et al., 2021</xref>), glutathione reductase (<xref ref-type="bibr" rid="ref43">Wang et al., 2019</xref>), thioredoxin reductase (<xref ref-type="bibr" rid="ref12">Hunter, 2014</xref>), SerT (<xref ref-type="bibr" rid="ref34">Tan et al., 2018</xref>), flavoprotein CsrF (<xref ref-type="bibr" rid="ref45">Xia et al., 2018</xref>), and fumarate reductase (<xref ref-type="bibr" rid="ref32">Song et al., 2017b</xref>) have been reported to be potentially involved in Se(IV) reduction in various bacterial species, suggesting the reduction of selenite occurs through diverse mechanisms. However, the current knowledge of the molecular mechanism of microbial selenite reduction is still limited. For example, it is largely unknown how bacterial cells respond to selenite stress and what molecular mechanism is utilized by microorganisms to reduce selenite. Therefore, the comprehensive studies of the mechanism of selenite reduction at the genome level by applying comparative transcriptomics analysis, microarray analysis, and proteomic analysis are urgently needed.</p>
<p>In the present study, the bacterial strain YS02 exhibiting an efficient selenite transformation ability was isolated from soil. Selenite reduction assay showed that strain YS02 can transform 93.2% of 5.0&#x2009;mM selenite to SeNPs within 24&#x2009;h, serving as an eco-friendly cell factory for the biogenesis of SeNPs. However, the exact molecular mechanism of selenite reduction by this strain is not clear. Therefore, the transcriptome response of YS02 cells exposed to sodium selenite (Na<sub>2</sub>SeO<sub>3</sub>) was investigated intensively using comparative transcriptomics analysis to clarify the possible mechanism of selenite reduction and biogenesis of SeNPs by the isolate YS02. Furthermore, the antibacterial activity of the SeNPs against Gram-negative and Gram-positive bacteria, such as <italic>Escherichia coli</italic> and <italic>Bacillus subtilis</italic>, was also investigated to explore the potential of the SeNPs as key assets in the future of healthcare.</p>
</sec>
<sec id="sec2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="sec3">
<title>Reagents and Medium</title>
<p>Sodium selenite (Na<sub>2</sub>SeO<sub>3</sub>) was obtained from Sigma-Aldrich (St. Louis, MO, United States). YEP (yeast extract peptone) broth was provided by Shanghai Gu Duo Biotechnology Co., Ltd. (Shanghai, China). All other analytical grade reagents used in present study were obtained from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China) and Solarbio Science and Technology Co., Ltd. (Beijing, China).</p>
</sec>
<sec id="sec4">
<title>Isolation and Identification of Selenite-Resistant Strains</title>
<p>Soil samples were taken from the seleniferous soil of Shitai county, ChiZhou, Anhui Province, China. The primary screening for microorganisms capable of reducing selenite to elemental Se was performed as described by <xref ref-type="bibr" rid="ref41">Wang et al. (2018b)</xref> with small modifications. Briefly, 0.1&#x2009;g of soil sample was suspended in sterile water (1&#x2009;ml) with continuous shaking at 180&#x2009;rpm at 30&#x00B0;C for 0.5&#x2009;h. Then, 100&#x2009;&#x03BC;l of the soil sample was serially diluted (10-fold) and placed on YEP plates supplemented with 10&#x2009;mM Na<sub>2</sub>SeO<sub>3</sub>. After incubating at 30&#x00B0;C for 48&#x2009;h, the colonies with a red color were selected and streak-cultured on new plates until pure cultures were obtained. Among the bacterial isolates, strain 02 (named YS02) was finally selected considering the most promising growth performance and selenite reduction activity.</p>
<p>Genomic DNA of strain YS02 was isolated using a Dzup Genomic DNA Isolation Kit (Sangon Biotech Co., Ltd., Shanghai, China) for the identification of isolate YS02. The 16S rRNA gene fragment amplification and sequencing were conducted as described by <xref ref-type="bibr" rid="ref11">Huang et al. (2021)</xref>. The obtained 16S rRNA gene sequence was then compared with sequences available on EzBioCloud server (<xref ref-type="bibr" rid="ref48">Yoon et al., 2017</xref>) and a phylogenetic tree based on maximum likelihood was constructed using the MEGA 7.0 software (<xref ref-type="bibr" rid="ref22">Kumar et al., 2016</xref>). The obtained 16S rRNA gene sequence was submitted to the GenBank database and has been assigned accession number MZ182304.</p>
</sec>
<sec id="sec5">
<title>Selenite Reduction and Production of SeNPs</title>
<p>The determination of SeO<sub>3</sub><sup>2&#x2212;</sup> reduction efficiency and the amount of Se<sup>0</sup> produced by isolate YS02 were performed following a previously established protocol (<xref ref-type="bibr" rid="ref41">Wang et al., 2018b</xref>). Briefly, isolate YS02 was cultured at 30&#x00B0;C in YEP medium containing 5.0&#x2009;mM selenite. Then, 10&#x2009;ml of bacterial culture was collected every 3&#x2009;h. The bacterial growth of the strain was calculated using the plate-counting method. For the selenite reduction assay and calculation of the amount of selenium (Se<sup>0</sup>) formed, samples were centrifuged at 12,000&#x2009;<italic>g</italic> for 20&#x2009;min. The remaining levels of Se(IV) were determined using ICP-OES (inductively coupled plasma optical emission spectrometry, Thermo Fisher Scientific, Waltham, MA, United States; <xref ref-type="bibr" rid="ref28">Nawaz et al., 2015</xref>). At the same time, spectrophotometry was applied to measure the Se<sup>0</sup> (<xref ref-type="bibr" rid="ref18">Khoei et al., 2017</xref>) in the pellet obtained after centrifugation.</p>
</sec>
<sec id="sec6">
<title>Localization of SeNPs</title>
<p>Isolate YS02 was cultured in YEP medium containing 5.0&#x2009;mM Na<sub>2</sub>SeO<sub>3</sub> (180&#x2009;rpm, 30&#x00B0;C). Bacterial cells cultured in YEP medium without Na<sub>2</sub>SeO<sub>3</sub> were set as a control. After incubation overnight, the samples were collected using gentle centrifugation (5,000&#x2009;<italic>g</italic>, 5&#x2009;min).</p>
<p>To use transmission electron microscopy (TEM), the pellets were fixed with glutaraldehyde (2% final concentration), placed onto carbon-coated copper grids and observed at 80.0&#x2009;kV on a transmission electron microscope (Hitachi HT-7700, Tokyo, Japan). For scanning electron microscopy (SEM), the pellets were fixed overnight at 4&#x00B0;C with glutaraldehyde (2.5% final concentration), followed by dehydration with a 30%, 50%, 70%, 80%, 95%, 100% ethanol gradient. Finally, the samples were processed for critical point drying and observed with a Hitachi S4800 SEM (Tokyo, Japan).</p>
</sec>
<sec id="sec7">
<title>SeNPs Preparation and Characterization</title>
<p>The preparation and purification of SeNPs from bacterial cultures of YS02 were conducted using a previously published protocol of <xref ref-type="bibr" rid="ref41">Wang et al. (2018b)</xref>. The particle size and zeta-potential of the obtained SeNPs were measured by dynamic light scattering (DLS; Zen 3600 Zetasizer Nano-ZS, Malvern Instruments Ltd., Worcestershire, United Kingdom; <xref ref-type="bibr" rid="ref24">Lampis et al., 2017</xref>). The chemical composition of the SeNPs was determined by energy-dispersive X-ray (EDX), while the morphology of the SeNPs was observed by SEM.</p>
<p>For FTIR spectroscopic analysis, SeNPs were separated from cells and cell debris in the bacterial culture after incubation with sodium selenite by centrifugation at 6,000&#x2009;<italic>g</italic> for 5&#x2009;min. After centrifugation, the supernatant was collected and filtered through a 0.22&#x2009;&#x03BC;m filter. Then, SeNPs were harvested by centrifuging the resulting filtered supernatant (40,000&#x2009;<italic>g</italic>; 30&#x2009;min); the obtained pellet was washed three times with ddH<sub>2</sub>O and finally resuspended in ddH<sub>2</sub>O; the suspension was dried in a vacuum freeze-drying system. A mid-infrared spectrum (4,000&#x2013;400&#x2009;cm<sup>&#x2212;1</sup>) of the freeze-dried SeNPs (in a KBr pellet, using KBr heated at 150&#x00B0;C for 5&#x2009;min prior to its use for pelleting, prepared at ambient conditions under a pressure of 20&#x2009;MPa for 40&#x2009;s) was recorded in the transmission mode using a Thermo Scientific Nicolet iS20 FTIR spectrometer (Waltham, MA, United States). The baseline-corrected spectroscopic data were collected and manipulated using the OMNIC software (ver. 8.2.0.387); no automatic smoothening was applied, as the spectrum was of appropriate quality.</p>
</sec>
<sec id="sec8">
<title>Antibacterial Activity of SeNPs</title>
<p>The antibacterial activity of SeNPs produced by strain YS02 was measured determined using the cup diffusion method as described by <xref ref-type="bibr" rid="ref1">Al Jahdaly et al. (2021)</xref>. To prepare water-dispersed SeNPs, 20&#x2009;mg of SeNPs were suspended in sterile ddH<sub>2</sub>O to obtain a concentration of 200&#x2009;mg/ml. Two Gram-positive bacteria including <italic>Staphylococcus epidermidis</italic> (ATCC-51625), and <italic>B. subtilis</italic> (ATCC-6633), and two Gram-negative bacteria including <italic>Pseudomonas aeruginosa</italic> (ATCC-47085), and <italic>E. coli</italic> (ATCC-8739), were used in this study. Briefly, the four bacteria were cultured in a shaking incubator (180&#x2009;rpm) at 30&#x00B0;C (<italic>P. aeruginosa</italic>) or 37&#x00B0;C (other organisms) for 24&#x2009;h, and then seeded in Petri dishes containing agar media. Then a droplet of 50&#x2009;&#x03BC;l of the SeNPs suspension or a Kanamycin solution (100&#x2009;&#x03BC;g/ml) was added onto filter paper disks (&#x00F8; 6&#x2009;mm) and left to dry. Finally, the disks with the investigated SeNPs and with the standard antibiotic were placed on the agar plates and incubated at 30&#x00B0;C (<italic>P. aeruginosa</italic>) or 37&#x00B0;C (other organisms). After 24&#x2009;h of incubation, the antibacterial activity was evaluated by measuring the size of the inhibition zone.</p>
</sec>
<sec id="sec9">
<title>Transcriptomic Analysis</title>
<sec id="sec10">
<title>Total RNA Extraction, Library Preparation, and Sequencing</title>
<p>Isolate YS02 was cultured under the same culture conditions in YEP medium containing 5.0&#x2009;mM selenite (selenite treatment) or without selenite (control). After batch culturing at 30&#x00B0;C for 14&#x2009;h, YS02 cells were harvested, quenched in liquid nitrogen immediately for 5&#x2009;min, and stored at &#x2212;80&#x00B0;C until use. The samples from control were defined as CK-1, CK-2, and CK-3, while samples from selenite treatment were set as Se-1, Se-2, and Se-3, respectively. The total RNA extraction, RNA integrity assessment, and cDNA library construction were conducted at Beijing Genomics Institute (BGI, Shenzhen, China) according to the methods described by <xref ref-type="bibr" rid="ref42">Wang et al. (2021)</xref>. Finally, RNA-<italic>sequencing</italic> of the cDNA library was carried out on a BGISEQ-500 platform (BGI, Shenzhen, China). After quality control and removing adaptor sequences/low-quality sequences (<xref ref-type="bibr" rid="ref33">Sun et al., 2019</xref>), the clean reads that were filtered from the raw reads were mapped to the reference genome sequences of <italic>P. mirabilis</italic> ATCC 29906 (genome assembly ASM16075v1) using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts). The raw data produced in the present study have been deposited in the National Center for Biotechnology Information (NCBI) database under the accession number PRJNA737579.</p>
</sec>
<sec id="sec11">
<title>Transcriptomic Analyses</title>
<p>The expression levels of different genes and transcripts were measured using FPKM (fragments per kilobase per million mapped fragments). Differential expression analysis between the two groups (CK vs. selenite treatment) was performed using the DESeq2 Bioconductor package. Gene abundance ratio log<sub>2</sub> (fold change; log<sub>2</sub>(FC))&#x2009;&#x2265;&#x2009;1 or&#x2009;&#x2264;&#x2009;&#x2212;1 and False Discovery Rate (FDR)&#x2009;&#x003C;&#x2009;0.05 were defined to be regulated differently. GO-Term Finder was used to identify gene ontology (GO) terms, and GO enrichment analysis was performed to evaluate significantly over-represented functional categories using Fisher&#x2019;s exact test with an FDR threshold of 5%. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was conducted to understand high-level functions and utilities of differentially expressed genes (DEGs; <xref ref-type="bibr" rid="ref49">Yu et al., 2019</xref>).</p>
</sec>
<sec id="sec12">
<title>Quantitative Real-Time PCR Validation</title>
<p>To verify the reliability of the transcriptome sequencing data, several representative DEGs were selected for quantitative analysis. These genes encode key enzymes involved in the glutathione and sulfur metabolism, pyruvate dehydrogenase system, and pentose phosphate pathway (PPP). Primer sequences used in this study are listed in <xref ref-type="supplementary-material" rid="SM2">Supplementary Table S2</xref>. Isolate YS02 was cultured in the condition that mimicked the conditions used for the RNAseq library preparation described above. The total RNA was isolated using a Total RNA Extraction Kit (Solarbio Science and Technology Co., Ltd., Beijing, China). Then PCR reactions were performed using One Step RT-qPCR Kit (Sangon Biotech Co., Ltd., Shanghai, China), in accordance with the manufacturer&#x2019;s protocol. The 16S rRNA gene was used as a reference gene, and the fold changes in target gene expression was calculated using the 2<sup>&#x2212;&#x0394;&#x0394;Ct</sup> method.</p>
</sec>
</sec>
</sec>
<sec id="sec13">
<title>Results and Discussion</title>
<sec id="sec14">
<title>Bacterial Strain Isolation and Identification</title>
<p>Microbial and enzymic activities in soil play a critical role in the global selenium cycle; thus, Se-rich sediments or soils are an ideal source for isolating selenite-reducing bacteria (<xref ref-type="bibr" rid="ref4">El-Ramady et al., 2015</xref>; <xref ref-type="bibr" rid="ref5">Eswayah et al., 2016</xref>). In this study, 15 bacterial strains were isolated from seleniferous soil. Of these, isolate 02 (YS02) showed the best growth performance on YEP plates containing 10&#x2009;mM Na<sub>2</sub>SeO<sub>3</sub>. BLAST search results indicated that the 16S rRNA gene sequence of strain YS02 exhibited 99% sequence similarity to that of <italic>Proteus mirabilis</italic> ATCC 29906(T). Furthermore, phylogenetic analysis also showed that strain YS02 belongs to the genus <italic>Proteus</italic>, with the highest similarity to <italic>P. mirabilis</italic> (<xref rid="fig1" ref-type="fig">Figure 1</xref>). Therefore, the strain YS02 was identified as <italic>Proteus</italic> sp. YS02. <italic>Proteus</italic> spp. are widely distributed in the environment, including animal guts, soils, and water. They possess the ability to tolerate or utilize polluting compounds (e.g., heavy metals and antibiotics) and promote plant growth. Moreover, several members of the genus <italic>Proteus</italic>, such as <italic>P. mirabilis</italic> YC801 (<xref ref-type="bibr" rid="ref40">Wang et al., 2018a</xref>) or <italic>P. hauseri</italic> QW4 (<xref ref-type="bibr" rid="ref17">Khalilian et al., 2015</xref>), have been reported to reduce selenite/selenate to Se<sup>0</sup> and biosynthesize SeNPs, allowing for the possibility of exploring these microorganisms in selenium bioremediation and synthesis of SeNPs. Therefore, the isolate YS02 was selected for subsequent study.</p>
<fig position="float" id="fig1">
<label>Figure 1</label>
<caption>
<p>Maximum likelihood tree inferred through MEGA 7 software based on 16S rRNA gene sequence of strain YS02 and related representative strains. <italic>Sphingobacterium zeae</italic> (KU201960) was used as the out-group member. The scale bars represent 0.05 substitutions per site.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g001.tif"/>
</fig>
</sec>
<sec id="sec15">
<title>Synthesis of SeNPs by <italic>Proteus</italic> sp. YS02 and Their Characterization</title>
<p>After cultivation of <italic>Proteus</italic> sp. YS02 in selenite-containing YEP culture medium, SeO<sub>3</sub><sup>2&#x2212;</sup> reduction and Se<sup>0</sup> formation were observed within 6&#x2009;h indicated by the formation of a reddish coloration in the culture medium that is a typical characteristic of microbially produced Se<sup>0</sup> (<xref rid="fig2" ref-type="fig">Figure 2A</xref>). Furthermore, it is interesting that the SeO<sub>3</sub><sup>2&#x2212;</sup> reduction and Se<sup>0</sup> biogenesis were in accordance with the strain growth kinetics; only 2.9% of the initial SeO<sub>3</sub><sup>2&#x2212;</sup> were reduced within 6&#x2009;h, while most of the remaining selenite (&#x003E;73%) was depleted during the exponential growth phase (between 9 and 15&#x2009;h), and then nearly exhausted after 24&#x2009;h of incubation (<xref rid="fig2" ref-type="fig">Figure 2B</xref>). Selenite reduction being tightly related to the bacterial growth phase has been reported for other bacteria, including <italic>Alcaligenes faecalis</italic> Se03 (<xref ref-type="bibr" rid="ref41">Wang et al., 2018b</xref>), <italic>S. maltophilia</italic> SeITE02 (<xref ref-type="bibr" rid="ref24">Lampis et al., 2017</xref>), and <italic>Lysinibacillus</italic> sp. (<xref ref-type="bibr" rid="ref50">Zhang et al., 2019</xref>), suggesting that reducing compounds and/or cellular reductases (whose secretion and consumption are inextricably associated with the growth state of the microbes; <xref ref-type="bibr" rid="ref41">Wang et al., 2018b</xref>) catalyze selenite reduction. Moreover, the depletion of SeO<sub>3</sub><sup>2&#x2212;</sup> was accompanied by the production of Se<sup>0</sup>&#x2014;after 24&#x2009;h of cultivation, about 93.2% of the initial selenite were transformed to Se<sup>0</sup> (<xref rid="fig2" ref-type="fig">Figure 2B</xref>). In contrast, no visible color change or Se<sup>0</sup> production was noted in control flasks that contained merely strain YS02 (see <xref rid="fig2" ref-type="fig">Figure 2A</xref>, right-hand flask) or selenite (data not shown), suggesting the active participation of bacterial isolate YS02 in selenite biotransformation and Se<sup>0</sup> production.</p>
<fig position="float" id="fig2">
<label>Figure 2</label>
<caption>
<p>Growth of bacterial strain YS02 in liquid YEP medium containing 5.0&#x2009;mM selenite. <bold>(A)</bold> Images of cultures with 5.0&#x2009;mM selenite (on the left) and without selenite (on the right) aerobically grown for 9&#x2009;h and <bold>(B)</bold> the growth curve, time courses of SeO<sub>3</sub><sup>2&#x2212;</sup> reduction, and Se<sup>0</sup> production by strain YS02. Each test was performed in triplicate, and data were presented as the mean&#x2009;&#x00B1;&#x2009;standard deviation.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g002.tif"/>
</fig>
<p>As many bacteria link the bioreduction of selenite to Se<sup>0</sup> with the production of SeNPs, we investigated whether <italic>Proteus</italic> sp. YS02 has the capacity to transform selenite to SeNPs. As shown in <xref rid="fig3" ref-type="fig">Figure 3</xref>, TEM analysis clearly revealed electron-dense nanoparticles (Se<sup>0</sup> nanoparticles) both inside and outside of the cells. However, the Se<sup>0</sup> nanoparticles could be observed mainly in the extracellular space (<xref rid="fig3" ref-type="fig">Figure 3C</xref>). Meanwhile, the formation of nanoparticles was not detected in cultures grown in the absence of selenite (<xref rid="fig3" ref-type="fig">Figure 3A</xref>). Interestingly, some extracellular nanoparticles appeared to be associated with empty ghost cells (cell walls appearing damaged; indicated by red arrows in <xref rid="fig3" ref-type="fig">Figure 3C</xref>), suggesting that this extracellular location is probably the consequence of cell lysis. Note that extracellular Se<sup>0</sup> nanoparticles have also been reported to be associated with empty ghost cells or cellular debris in other bacteria, such as <italic>Vibrio natriegens</italic> (<xref ref-type="bibr" rid="ref7">Fern&#x00E1;ndez-Llamosas et al., 2017</xref>), <italic>S. maltophilia</italic> SeITE02 (<xref ref-type="bibr" rid="ref24">Lampis et al., 2017</xref>), and <italic>Bacillus mycoides</italic> SeITE01 (<xref ref-type="bibr" rid="ref23">Lampis et al., 2014</xref>), which indicates that cell lysis may cause the release of intracellularly formed Se<sup>0</sup> nanoparticles in these bacteria. Moreover, SEM analyses (<xref rid="fig4" ref-type="fig">Figures 4A,B</xref>) also confirmed the presence of extracellular Se<sup>0</sup> nanoparticles (<xref rid="fig4" ref-type="fig">Figure 4B</xref>, white arrows). The micrographs showed an accumulation of electron-dense particles attached to the outer side of the external cell, while these particles were not observed in the cells grown on YEP without the selenite (see <xref rid="fig4" ref-type="fig">Figure 4A</xref>). Moreover, the Se<sup>0</sup> nanoparticles appeared spherical in shape and decidedly dishomogeneous in terms of size.</p>
<fig position="float" id="fig3">
<label>Figure 3</label>
<caption>
<p>TEM analysis of <italic>Proteus</italic> sp. YS02 <bold>(A)</bold> cultured without Na<sub>2</sub>SeO<sub>3</sub> and <bold>(B,C)</bold> cultured with 5&#x2009;mM Na<sub>2</sub>SeO<sub>3</sub> after 24&#x2009;h of incubation. White arrows show nanoparticles inside <bold>(B)</bold> or outside <bold>(C)</bold> the cells. Empty ghost cells are indicated by red arrows <bold>(C)</bold>. The bar represents 1&#x2009;&#x03BC;m.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g003.tif"/>
</fig>
<fig position="float" id="fig4">
<label>Figure 4</label>
<caption>
<p>SEM analysis of <italic>Proteus</italic> sp. YS02 <bold>(A)</bold> cultured without Na<sub>2</sub>SeO<sub>3</sub> and <bold>(B)</bold> cultured with 5&#x2009;mM Na<sub>2</sub>SeO<sub>3</sub> for 24&#x2009;h. White arrows indicate the produced extracellularly located nanoparticles. The bar represents 1&#x2009;&#x03BC;m.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g004.tif"/>
</fig>
<p>The produced Se<sup>0</sup> nanoparticles were purified and further analyzed by SEM&#x2013;EDX analysis. As shown in <xref rid="fig5" ref-type="fig">Figure 5</xref>, the purified SeNPs appear as spherical nanoparticles of varied sizes. The EDX spectra also clearly confirmed the presence of selenium&#x2014;the spherical nanoparticles exhibit Se-specific absorption peaks at 1.37, 11.22, and 12.49&#x2009;keV. Moreover, DLS analysis of purified SeNPs revealed an average dimension of 140&#x2009;&#x00B1;&#x2009;43&#x2009;nm, similar to those found in <italic>Azoarcus</italic> sp. CIB (174&#x2009;&#x00B1;&#x2009;36&#x2009;nm; <xref ref-type="bibr" rid="ref6">Fern&#x00E1;ndez-Llamosas et al., 2016</xref>) and in <italic>V. natriegens</italic> (136&#x2009;&#x00B1;&#x2009;31&#x2009;nm; <xref ref-type="bibr" rid="ref7">Fern&#x00E1;ndez-Llamosas et al., 2017</xref>). More, the produced SeNPs revealed a negative zeta-potential (&#x2212;34.2&#x2009;mV), suggesting the colloidal stability of SeNPs in the water phase.</p>
<fig position="float" id="fig5">
<label>Figure 5</label>
<caption>
<p>SEM&#x2013;EDX analysis of purified SeNPs produced by <italic>Proteus</italic> sp. YS02. The bar represents 5&#x2009;&#x03BC;m.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g005.tif"/>
</fig>
<p>In order to investigate the possible existence of bioorganic capping layers that could contribute to the synthesis and stability of SeNPs, FTIR spectroscopic analysis of the isolated and purified SeNPs was performed (<xref rid="fig6" ref-type="fig">Figure 6</xref>). This technique is highly sensitive to the presence of biomaterials covering the SeNPs surface and has been widely used for their characterization (see, e.g., <xref ref-type="bibr" rid="ref15">Kamnev et al. (2017</xref>, <xref ref-type="bibr" rid="ref14">2021)</xref>, <xref ref-type="bibr" rid="ref38">Tugarova et al. (2018)</xref> and references cited therein). The FTIR spectrum in <xref rid="fig6" ref-type="fig">Figure 6</xref> shows a number of absorption bands typically observed for biogenic SeNPs of microbial origin. The main important bands include: a very strong broad non-symmetric envelope around 3,600&#x2013;3,200&#x2009;cm<sup>&#x2212;1</sup> (featuring stretching vibrations of H-bonded O&#x2013;H and N&#x2013;H moieties); a series of bands at ~3,000&#x2013;2,800&#x2009;cm<sup>&#x2212;1</sup> (various characteristic stretching vibrations of C&#x2013;H bonds in alkanoic groups); weak but typical bands at 1,741&#x2009;cm<sup>&#x2212;1</sup> (stretching vibrations of the C=O group in ester moieties), 1,451&#x2009;cm<sup>&#x2212;1</sup> (bending vibrations of &#x2013;CH<sub>3</sub>/&#x2013;CH<sub>2</sub>&#x2013; groups) and 1,389&#x2009;cm<sup>&#x2212;1</sup> (symmetric stretching vibrations of carboxylic &#x2013;COO<sup>&#x2212;</sup> groups in amino acid side chains and/or carboxylated polysaccharides); a characteristic pair of bands between 1,637 and 1,537&#x2009;cm<sup>&#x2212;1</sup> (the amide I and II bands of proteins, respectively); a series of overlapping bands at ~1,200&#x2013;950&#x2009;cm<sup>&#x2212;1</sup> featuring polysaccharides and, occasionally, phosphate moieties (<xref ref-type="bibr" rid="ref15">Kamnev et al., 2017</xref>, <xref ref-type="bibr" rid="ref14">2021</xref>; <xref ref-type="bibr" rid="ref38">Tugarova et al., 2018</xref>).</p>
<fig position="float" id="fig6">
<label>Figure 6</label>
<caption>
<p>Fourier transform infrared spectrum of isolated SeNPs produced by <italic>Proteus</italic> sp. YS02.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g006.tif"/>
</fig>
<p>Thus, in accordance with the FTIR spectroscopic data, the biomacromolecular composition of the obtained biogenic SeNPs most likely includes proteins (for which the amide I and II bands mentioned above are accompanied by the weaker absorption around 1,240&#x2009;cm<sup>&#x2212;1</sup> featuring another typical protein-related band, amide III; <xref ref-type="bibr" rid="ref15">Kamnev et al., 2017</xref>, <xref ref-type="bibr" rid="ref14">2021</xref>; <xref ref-type="bibr" rid="ref38">Tugarova et al., 2018</xref>), polysaccharides (see the increased O&#x2013;H stretching envelope together with the characteristic region at ~1,200&#x2013;950&#x2009;cm<sup>&#x2212;1</sup>) and lipids (featured by a combination of stretching and bending C&#x2013;H vibrations with the ester carbonyl band at 1,741&#x2009;cm<sup>&#x2212;1</sup>). As was mentioned above, these biomacromolecular components are often found in surface capping layers of SeNPs produced by various microorganisms.</p>
<p>Note that carboxylic groups (featured by the weak band at 1,389&#x2009;cm<sup>&#x2212;1</sup> ascribed to their symmetric stretching vibrations; the accompanying antisymmetric vibrations of variable location at higher wavenumbers are known to be often masked by stronger amide I/amide II bands; <xref ref-type="bibr" rid="ref15">Kamnev et al., 2017</xref>, <xref ref-type="bibr" rid="ref14">2021</xref>; <xref ref-type="bibr" rid="ref38">Tugarova et al., 2018</xref>) are responsible for the negative zeta potentials typically found for such SeNPs in aqueous suspensions (<xref ref-type="bibr" rid="ref37">Tugarova and Kamnev, 2017</xref>). Finally, traces of water (which can form strong H-bonds with polar biomolecular groups and thus might be not fully removed by freeze-drying; see &#x201C;SeNPs Preparation and Characterization&#x201D;) could contribute to the increased stretching O&#x2013;H region (3,600&#x2013;3,200&#x2009;cm<sup>&#x2212;1</sup>) as well as indirectly to the amide I region by its bending (scissoring) H&#x2013;O&#x2013;H vibrations which are observed at ~1,640&#x2013;1,650&#x2009;cm<sup>&#x2212;1</sup> (<xref ref-type="bibr" rid="ref14">Kamnev et al., 2021</xref>).</p>
</sec>
<sec id="sec16">
<title>Antibacterial Activity</title>
<p>So far, a lot of metallic and metalloid nanoparticles have been reported to possess antimicrobial activity and thus can be exploited for alternative medicine therapy against multidrug-resistant pathogenic microbes. To evaluate potential biomedical utilizations of the SeNPs produced by YS02, their antibacterial activity against different specific strains including both Gram-negative (<italic>P. aeruginosa</italic> and <italic>E. coli</italic>) and Gram-positive (<italic>B. subtilis</italic> and <italic>S. epidermidis</italic>) bacteria was evaluated by the plate antibacterial test.</p>
<p>As shown in <xref rid="fig7" ref-type="fig">Figure 7</xref>, SeNPs at a specific concentration could effectively inhibit the microbial growth. Furthermore, it is interesting that the growth of the Gram-negative bacteria (<italic>P. aeruginosa</italic> and <italic>E. coli</italic>) was more influenced by the SeNPs compared to that of the Gram-positive bacteria as indicated by corresponding inhibition zones. Application of antibiotic (Kanamycin) provided the highest growth inhibition zones with sizes of 18.4&#x2009;mm and 22.9&#x2009;mm for <italic>E. coli</italic> and <italic>P. aeruginosa</italic>, respectively. However, the SeNPs also showed significant antibacterial effect with inhibition zone sizes between 13.5 and 12.5&#x2009;mm for <italic>E. coli</italic> and <italic>P. aeruginosa</italic>, respectively. For the Gram-positive bacteria, smaller inhibition zones were observed after the application of SeNPs: the sizes of inhibition zones were 11.9&#x2009;mm for <italic>B. subtilis</italic> and 9.8&#x2009;mm for <italic>S. epidermidis</italic>. Similarly, it was also found that the growth of <italic>E. coli</italic> and <italic>P. aeruginosa</italic> was most influenced by PVA/Chitosan/SeNPs nanocomposite while the effect on <italic>B. subtilis</italic> was the lowest (<xref ref-type="bibr" rid="ref25">Menazea et al., 2020</xref>). These results could be attributed to the distinct differences in the cell wall structure/cell surface between Gram-positive and Gram-negative bacteria&#x2014;the former have a stronger molecular network in the cell wall, which could present more difficulties for selenite ions to penetrate the cell than in Gram-negative bacteria (<xref ref-type="bibr" rid="ref36">Truong et al., 2021</xref>). It has recently been reported that the bactericidal activity of SeNPs can be explained in terms of changing the membrane potential, depleting ATP, promoting ROS production, and disrupting the membrane (<xref ref-type="bibr" rid="ref10">Huang et al., 2020</xref>).</p>
<fig position="float" id="fig7">
<label>Figure 7</label>
<caption>
<p>The antibacterial effect of isolated SeNPs (produced by <italic>Proteus</italic> sp. YS02) on <italic>E. coli</italic>, <italic>P. aeruginosa</italic>, <italic>B. subtilis</italic>, and <italic>S. epidermidis</italic> screened by the plate antibacterial test. The red colored disks represented SeNPs and the white disks represented the standard antibiotic.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g007.tif"/>
</fig>
<p>Overall, the findings reported in the present study indicate that the SeNPs produced by YS02 have a strong bactericidal effect on the pathogenic bacteria and have a potential to be used as a substitute for antibiotics in clinical applications. However, further research is needed to address the precise mechanism of the antibacterial action of the SeNPs.</p>
</sec>
<sec id="sec17">
<title>Overview of <italic>Proteus</italic> sp. YS02 Transcriptomic Profile</title>
<p>Although selenite reduction mechanisms and SeNPs synthesis have been studied in several bacterial species, they have not been completely clarified (<xref ref-type="bibr" rid="ref37">Tugarova and Kamnev, 2017</xref>; <xref ref-type="bibr" rid="ref39">Tugarova et al., 2020</xref>). The global transcriptome of the <italic>Proteus</italic> sp. YS02 cells was analyzed by RNA-seq technology to clarify the molecular mechanism of selenite reduction and production of SeNPs. Overall, six libraries (CK-1, CK-2, CK-3, Se-1, Se-2, and Se-3) were generated and sequenced using a DNBSEQ-T7 sequencer, and about 255 million pair-end clean reads (2&#x2009;&#x00D7;&#x2009;150&#x2009;bp long) were obtained. The number and quality scores of the aligned reads are shown in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S1</xref> and were sufficient to ensure the accuracy of the assembly and coverage.</p>
</sec>
<sec id="sec18">
<title>Transcriptional Data Analysis</title>
<p>After assembling using Bowtie2, a total of 3,153 transcripts were screened and used for DEGs identification. Following comparison with CK (control sample without Se treatment), a total of 473 DEGs were found to have been expressed during Se treatment, among which 197 genes were significantly upregulated, and 276 genes were significantly downregulated (<xref rid="fig8" ref-type="fig">Figure 8</xref>). Based on GO functional analyses, these DEGs could be classified into three main GO categories, including molecular functions (MF), biological processes (BP), and cellular components (CC). For the 197 upregulated genes, DEGs enriched in BP mainly included cellular processes (52.8%), metabolic processes (52.8%), and localization (10.7%). CC DEGs were related to the cell (36.5%), membrane (28.4%), and membrane parts (24.9%), and MF DEGs were associated with catalytic activity (63.5%), binding (47.7%), and transporter activity (9.1%). The most obvious differences for the 276 downregulated genes of BP were those related to metabolic processes (45.3%), cellular processes (42.4%), and localization (14.9%); the most obvious differences of CC were also associated with the cell (43.8%), membrane (35.5%), membrane parts (33.0%), and macromolecular complexes (14.1%). The most obvious differences of MF were mainly concentrated in catalytic activity (47.1%), binding (42.4%), transporter activity (15.6%), and structural molecule activity (8.3%). GO enrichment of the top 20 GO terms showed that the functional proteins involved in the cellular response to stress (GO: 0033554), DNA metabolic process (GO: 0006259), ATPase-coupled sulfate transmembrane transporter (GO: 0015419), and ATP binding (GO: 0005524) were enhanced fundamentally in the presence of selenite, while genes assigned to macromolecular complexes (GO: 0032991), ribosomes (GO: 0005840), cytoplasmic parts (GO: 0044444), energy derivation (GO: 0015980), and the tricarboxylic acid cycle (GO: 0006099) were significantly downregulated (<xref rid="fig9" ref-type="fig">Figure 9</xref>).</p>
<fig position="float" id="fig8">
<label>Figure 8</label>
<caption>
<p>The volcano plots of genes for <italic>Proteus</italic> sp. YS02 between the control and Se treatment. Red and blue dots represent genes that were significantly upregulated and downregulated, respectively. Gray dots indicate the genes without significant differential expression.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g008.tif"/>
</fig>
<fig position="float" id="fig9">
<label>Figure 9</label>
<caption>
<p>GO classifications of <bold>(A)</bold> downregulated DEGs and <bold>(B)</bold> upregulated DEGs. The X axis presents the number of DEGs belonging to specific categories. The Y axis presents three major functional categories of GO terms.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g009.tif"/>
</fig>
</sec>
<sec id="sec19">
<title>KEGG Pathway Enrichment Analysis</title>
<p>KEGG pathway enrichment analysis for DEGs has shown that complicated metabolic pathways participated in the response to selenium stress. As shown in <xref rid="fig10" ref-type="fig">Figure 10A</xref>, the pathways that were significantly enriched among the upregulated DEGs included sulfur metabolism (ko00920, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05), purine metabolism (ko00230, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05), and histidine metabolism (ko00340, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05). The pathways involved in the biosynthesis of antibiotics (ko01130), pyrimidine metabolism (ko00240), and the PPP (ko00030) also had high enrichment scores but were not considered as significant. Furthermore, the enriched KEGG pathways for the downregulated DEGs between the control group and Se treatment group are shown in <xref rid="fig10" ref-type="fig">Figure 10B</xref>. ABC transporters (ko02010, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05), oxidative phosphorylation (ko00190, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05), carbon metabolism (ko01200, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05), and the citrate cycle (TCA cycle; ko00020, <italic>p</italic>&#x2009;&#x003C;&#x2009;0.05) were the most enriched pathways.</p>
<fig position="float" id="fig10">
<label>Figure 10</label>
<caption>
<p>Enriched KEGG pathways for <bold>(A)</bold> upregulated DEGs and <bold>(B)</bold> downregulated DEGs in the presence of selenite. The X axis corresponds to the percentage of DEGs belonging to a specific pathway. The Y axis presents the names of the top 20 pathways.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g010.tif"/>
</fig>
</sec>
<sec id="sec20">
<title>The Main Genes Participating in Selenite Reduction and SeNPs Biosynthesis</title>
<p>Since selenium is one of the chalcogen elements, it is proposed that reductases in sulfur metabolic pathways may catalyze the reduction of Se(IV; <xref ref-type="bibr" rid="ref34">Tan et al., 2018</xref>; <xref ref-type="bibr" rid="ref11">Huang et al., 2021</xref>). In this study, the expressions of genes responsible for sulfate assimilation metabolism were significantly upregulated in the presence of selenite. The ABC transporter complex CysAWTP is composed of two CysA ATP-binding proteins, two transmembrane proteins (CysT and CysW), and a CysP solute-binding protein. It has been reported to be responsible for sulfate/thiosulfate import in many microbes (<xref ref-type="bibr" rid="ref9">Han and Lee, 2006</xref>). It is interesting that selenite treatment upregulated expression of <italic>cysA</italic>, <italic>cysW</italic>, <italic>cysU</italic>, and <italic>CysP</italic> (the fold changes were 2.50, 2.79, 2.64, and 2.58 log<sub>2</sub>(FC) while comparing Se vs. CK, respectively), suggesting the sulfate transport system permease is responsible for the transmembrane transport of selenite in <italic>Proteus</italic> sp. YS02. The uptake and transport of selenite in <italic>E. coli</italic> have also been reported to be controlled by the sulfate transport complex ABC encoded by the <italic>cysAWTP</italic> operon (<xref ref-type="bibr" rid="ref37">Tugarova and Kamnev, 2017</xref>). Furthermore, the gene expressions of <italic>cysN</italic> (encoding sulfate adenylyltransferase subunit 1), <italic>cysD</italic> (encoding sulfate adenylyltransferase subunit 2), <italic>cysH</italic> (encoding phosphoadenosine phosphosulfate reductase), <italic>cysJ</italic> [encoding sulfite reductase (NADPH) flavoprotein alpha-component], and <italic>cysI</italic> [encoding sulfite reductase (NADPH) hemoprotein beta-component], were all significantly upregulated (2.27, 2.65, 3.62, 3.59, and 3.69-fold, respectively). Sulfite reductase (cysJI in this case) was reported to catalyze the reduction of selenite/selenate to Se<sup>0</sup> with NAD(P)H serving as an electron donor in bacterial isolates <italic>Providencia rettgeri</italic> HF16 (<xref ref-type="bibr" rid="ref11">Huang et al., 2021</xref>) and <italic>C. testosteroni</italic> S44 (<xref ref-type="bibr" rid="ref34">Tan et al., 2018</xref>). Similarly, in this study, the <italic>CysJ</italic> and <italic>CysI</italic> expression was significantly upregulated in the presence of selenite, suggesting that selenite is more likely to be transformed <italic>via</italic> a sulfite reductase-mediated metabolic pathway in YS02.</p>
<p>The PPP is one of the major sources of reducing power (NADPH) and metabolic intermediates that are required for biosynthetic processes (<xref ref-type="bibr" rid="ref21">Kruger and von Schaewen, 2003</xref>; <xref ref-type="bibr" rid="ref44">Wushensky et al., 2018</xref>). It is interesting that genes involved in the PPP pathway, such as <italic>zwf</italic> (encoding glucose-6-phosphate 1-dehydrogenase), <italic>deoC</italic> (encoding deoxyribose-phosphate aldolase), <italic>tktA</italic> (encoding transketolase), and deo<italic>B</italic> (encoding phosphopentomutase), were significantly upregulated. Furthermore, the expression of <italic>aceE</italic> (encoding pyruvate dehydrogenase E1 component) and <italic>pdhC</italic> (encoding pyruvate dehydrogenase E2 component) were also upregulated in the presence of selenite. The pyruvate dehydrogenase system catalyzes the oxidative decarboxylation of pyruvate with the production of acetyl coenzyme A (acetyl-CoA), NADH, and CO<sub>2</sub> (<xref ref-type="bibr" rid="ref16">Karsten et al., 2002</xref>). Taken together, the significant enhancement of the PPP genes and pyruvate dehydrogenase under selenite treatment confirmed their involvement in selenite biotransformation by supplying reducing equivalents and enhancing energy metabolism.</p>
<p>Additionally, the reduction and detoxification of selenite ions by microbes may be accompanied by the production of reactive oxygen species that can damage cell membranes or DNA (<xref ref-type="bibr" rid="ref35">Tetteh et al., 2014</xref>; <xref ref-type="bibr" rid="ref51">Zhao et al., 2018</xref>). It is noteworthy that the expression of several genes encoding enzymes classified as oxidoreductases and transferases, such as <italic>nrd</italic> (encoding ribonucleoside-diphosphate reductase), <italic>hcp</italic> (encoding hydroxylamine reductase), <italic>cysG</italic> (encoding uroporphyrin-III C-methyltransferase), <italic>ndh</italic> (encoding NADH dehydrogenase), and <italic>hisG</italic> (encoding ATP phosphoribosyltransferase) were also upregulated, indicating that these enzymes may be associated with oxidative stress defense and maintenance of redox homeostasis in strain YS02. However, the expression of several expected antioxidant protein-encoding genes, such as <italic>gsh</italic> (encoding glutathione synthetase), <italic>gor</italic> (encoding glutathione reductase), <italic>gorA</italic> (encoding glutathione-disulfide reductase), <italic>sodB</italic> (encoding superoxide dismutase), <italic>trxA</italic> (encoding thioredoxin), and <italic>trxB</italic> (encoding thioredoxin reductase), showed no significant change under selenite treatment. This was similar to the findings of <xref ref-type="bibr" rid="ref32">Song et al. (2017b)</xref>, who showed that selenite treatment caused a 2.42-fold increase in fumarate reductase abundance but had no effect on the expression of <italic>gsh</italic>, <italic>gor</italic>, or <italic>trxB</italic>.</p>
</sec>
<sec id="sec21">
<title>Validation of Candidate Genes Expression by qRT-PCR</title>
<p>The relative expressions of 10 selected DEGs were determined using RT-qPCR (<xref ref-type="supplementary-material" rid="SM2">Supplementary Table S2</xref>) to validate the RNA-seq sequencing results. The candidate DEGs included <italic>cysN</italic>&#xFF0C;<italic>CysA</italic>&#xFF0C;<italic>CysP, CysI, CysJ</italic>&#xFF0C;<italic>metF</italic> (encoding methylenetetrahydrofolate reductase), <italic>dppB</italic> (encoding dipeptide transport system permease), <italic>frdC</italic> (encoding fumarate reductase subunit C), <italic>frdD</italic> (encoding fumarate reductase subunit D), and <italic>sdhA</italic> (encoding succinate dehydrogenase flavoprotein subunit). Overall, the upregulation or downregulation of the tested genes were consistent with the results obtained by transcriptome analysis, which indicated that the latter were reliable.</p>
</sec>
<sec id="sec22">
<title>Mechanism Dominating Selenite Reduction and SeNPs Production in <italic>Proteus</italic> sp. YS02</title>
<p>A model for selenite reduction and SeNPs production in <italic>Proteus</italic> sp. YS02 was proposed based on the above analysis. First, the sulfate transporter system (CysPUWA) is predicted to be involved in the uptake of Se(IV) from the extracellular fluid into the cytoplasm. Meanwhile, the PPP and pyruvate dehydrogenase were also activated under selenite treatment and thus produced NADPH or NADH, providing more reducing power for selenite reduction. The produced NADPH or NADH is then transported to sulfite reductase to favor the subsequent reaction. Finally, the reduction of Se(IV) to Se<sup>0</sup> is accomplished by sulfite reductase (CysIJ in this case) with NADPH or NADH serving as the electron donor (<xref rid="fig11" ref-type="fig">Figure 11</xref>). Notably, TEM analysis detected Se<sup>0</sup> nanoparticles both inside and outside of the cells and empty ghost cells, suggesting the produced SeNPs in the cytoplasm may be subsequently released into the extracellular space through cell lysis or by other vesicular secretion systems, as reported for other bacteria such as <italic>V. natriegens</italic> (<xref ref-type="bibr" rid="ref7">Fern&#x00E1;ndez-Llamosas et al., 2017</xref>). However, further research is needed to elucidate the mechanism responsible for the release of Se<sup>0</sup> nanoparticles.</p>
<fig position="float" id="fig11">
<label>Figure 11</label>
<caption>
<p>A hypothesized mechanism of selenite biotransformation and biosynthesis of SeNPs in strain <italic>Proteus</italic> sp. YS02. Yet unidentified processes are shown in dotted lines or question mark.</p>
</caption>
<graphic xlink:href="fmicb-13-845321-g011.tif"/>
</fig>
</sec>
</sec>
<sec id="sec23" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/<xref ref-type="supplementary-material" rid="SM1">Supplementary Material</xref>.</p>
</sec>
<sec id="sec24">
<title>Author Contributions</title>
<p>YW and QY: conceptualization. YW: methodology and investigation. YS, YJ, and BM: software. JD and JC: data curation. AT and AK: FTIR spectroscopic analysis and interpretation. SH: writing&#x2013;original draft preparation, supervision, and project administration. SH and AK: writing&#x2013;review and editing. YW and SH: funding acquisition. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="sec41" sec-type="funding-information">
<title>Funding</title>
<p>This work was supported by the Anhui Provincial Natural Science Foundation, China (2108085QC88 and 2008085MC60), and the Key projects of Anhui Provincial Department of Education (KJ2021A0881). The work of AT and AK was carried out under research theme no. 121032300311-5 of the Russian Academy of Sciences. The funding organizations had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</p>
</sec>
<sec id="conf1" 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="sec27" 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>
</body>
<back>
<sec id="sec26" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at:</p> <p><ext-link xlink:href="https://www.frontiersin.org/articles/10.3389/fmicb.2022.845321/full#supplementary-material" ext-link-type="uri">https://www.frontiersin.org/articles/10.3389/fmicb.2022.845321/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Table_1.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table_2.docx" id="SM2" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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