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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High quality draft genome sequence of the heavy metal resistant bacterium <italic>Halomonas zincidurans</italic> type strain B6<sup>T</sup></title><author><name sortKey="Huo, Ying Yi" sort="Huo, Ying Yi" uniqKey="Huo Y" first="Ying-Yi" last="Huo">Ying-Yi Huo</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Li, Zheng Yang" sort="Li, Zheng Yang" uniqKey="Li Z" first="Zheng-Yang" last="Li">Zheng-Yang Li</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Cheng, Hong" sort="Cheng, Hong" uniqKey="Cheng H" first="Hong" last="Cheng">Hong Cheng</name><affiliation><nlm:aff id="I2">College of Life Sciences, Zhejiang University, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Wang, Chun Sheng" sort="Wang, Chun Sheng" uniqKey="Wang C" first="Chun-Sheng" last="Wang">Chun-Sheng Wang</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Xu, Xue Wei" sort="Xu, Xue Wei" uniqKey="Xu X" first="Xue-Wei" last="Xu">Xue-Wei Xu</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25945155</idno><idno type="pmc">4286145</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286145</idno><idno type="RBID">PMC:4286145</idno><idno type="doi">10.1186/1944-3277-9-30</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000299</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000299</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">High quality draft genome sequence of the heavy metal resistant bacterium <italic>Halomonas zincidurans</italic> type strain B6<sup>T</sup></title><author><name sortKey="Huo, Ying Yi" sort="Huo, Ying Yi" uniqKey="Huo Y" first="Ying-Yi" last="Huo">Ying-Yi Huo</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Li, Zheng Yang" sort="Li, Zheng Yang" uniqKey="Li Z" first="Zheng-Yang" last="Li">Zheng-Yang Li</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Cheng, Hong" sort="Cheng, Hong" uniqKey="Cheng H" first="Hong" last="Cheng">Hong Cheng</name><affiliation><nlm:aff id="I2">College of Life Sciences, Zhejiang University, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Wang, Chun Sheng" sort="Wang, Chun Sheng" uniqKey="Wang C" first="Chun-Sheng" last="Wang">Chun-Sheng Wang</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author><author><name sortKey="Xu, Xue Wei" sort="Xu, Xue Wei" uniqKey="Xu X" first="Xue-Wei" last="Xu">Xue-Wei Xu</name><affiliation><nlm:aff id="I1">Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</nlm:aff></affiliation></author></analytic><series><title level="j">Standards in Genomic Sciences</title><idno type="eISSN">1944-3277</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Halomonas zincidurans</italic> strain B6<sup>T</sup> was isolated from a deep-sea heavy metal rich sediment from the South Atlantic Mid-Ocean Ridge. The strain showed significant resistance to heavy metals, especially to zinc. Here we describe the genome sequence and annotation, as well as the features, of the organism. The genome contains 3,325 protein-coding genes (2,848 with predicted functions), 61 tRNA genes and 6 rRNA genes. <italic>H. zincidurans</italic> strain B6<sup>T</sup> encodes 31 genes related to heavy metal resistance. And HGT may play an important role in its adaption to the heavy metal rich environment. <italic>H. zincidurans</italic> strain B6<sup>T</sup> may have potential applications in the bioremediation of heavy metal-contaminated environments.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Valls, M" uniqKey="Valls M">M Valls</name></author><author><name sortKey="De Lorenzo, V" uniqKey="De Lorenzo V">V de Lorenzo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nies, Dh" uniqKey="Nies D">DH Nies</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ozdemir, S" uniqKey="Ozdemir S">S Özdemir</name></author><author><name sortKey="Kilinc, E" uniqKey="Kilinc E">E Kilinc</name></author><author><name sortKey="Poli, A" uniqKey="Poli A">A Poli</name></author><author><name sortKey="Nicolaus, B" uniqKey="Nicolaus B">B Nicolaus</name></author><author><name sortKey="Guven, K" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Stand Genomic Sci</journal-id><journal-id journal-id-type="iso-abbrev">Stand Genomic Sci</journal-id><journal-title-group><journal-title>Standards in Genomic Sciences</journal-title></journal-title-group><issn pub-type="epub">1944-3277</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25945155</article-id><article-id pub-id-type="pmc">4286145</article-id><article-id pub-id-type="publisher-id">1944-3277-9-30</article-id><article-id pub-id-type="doi">10.1186/1944-3277-9-30</article-id><article-categories><subj-group subj-group-type="heading"><subject>Short Genome Report</subject></subj-group></article-categories><title-group><article-title>High quality draft genome sequence of the heavy metal resistant bacterium <italic>Halomonas zincidurans</italic> type strain B6<sup>T</sup></article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Huo</surname><given-names>Ying-Yi</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>yingyihuo@gmail.com</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Li</surname><given-names>Zheng-Yang</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>zhengyangli@gmail.com</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Cheng</surname><given-names>Hong</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>hongcheng@gmail.com</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Wang</surname><given-names>Chun-Sheng</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>wangsio@sio.org.cn</email></contrib><contrib contrib-type="author" corresp="yes" id="A5"><name><surname>Xu</surname><given-names>Xue-Wei</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>xuxw@sio.org.cn</email></contrib></contrib-group><aff id="I1"><label>1</label>Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China</aff><aff id="I2"><label>2</label>College of Life Sciences, Zhejiang University, Hangzhou, P. R. China</aff><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>29</day><month>12</month><year>2014</year></pub-date><volume>9</volume><fpage>30</fpage><lpage>30</lpage><history><date date-type="received"><day>9</day><month>7</month><year>2014</year></date><date date-type="accepted"><day>23</day><month>11</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Huo et al.; licensee BioMed Central.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Huo et al.; licensee BioMed Central.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><self-uri xlink:href="http://www.standardsingenomics.com/content/9/1/30"></self-uri><abstract><p><italic>Halomonas zincidurans</italic> strain B6<sup>T</sup> was isolated from a deep-sea heavy metal rich sediment from the South Atlantic Mid-Ocean Ridge. The strain showed significant resistance to heavy metals, especially to zinc. Here we describe the genome sequence and annotation, as well as the features, of the organism. The genome contains 3,325 protein-coding genes (2,848 with predicted functions), 61 tRNA genes and 6 rRNA genes. <italic>H. zincidurans</italic> strain B6<sup>T</sup> encodes 31 genes related to heavy metal resistance. And HGT may play an important role in its adaption to the heavy metal rich environment. <italic>H. zincidurans</italic> strain B6<sup>T</sup> may have potential applications in the bioremediation of heavy metal-contaminated environments.</p></abstract><kwd-group><kwd><italic>Halomonas</italic></kwd><kwd>Heavy metal resistant</kwd><kwd>The South Atlantic Ocean</kwd><kwd>Genome</kwd></kwd-group></article-meta></front><body><sec sec-type="intro"><title>Introduction</title><p>Heavy metals, either essential (e.g. Mn, Zn, Cu, Co, Ni and Mo) or toxic (e.g. Hg, Ag and Cd), are generally harmful to microbial cells even at low concentrations, as to other living organisms [<xref ref-type="bibr" rid="B1">1</xref>,<xref ref-type="bibr" rid="B2">2</xref>]. However, some microorganisms are able to resist to certain kinds and concentrations of heavy metals through several mechanisms, such as incorporating or precipitating heavy metals into complexes, oxidizing or reducing metals to less toxic valence states, and direct transporting metals out of the cell [<xref ref-type="bibr" rid="B3">3</xref>,<xref ref-type="bibr" rid="B4">4</xref>]. These heavy metal resistant microorganisms have been attracting great interests because of their potential biotechnological applications in bio-mining of expensive heavy metals and bioremediation of heavy metal-contaminated environment [<xref ref-type="bibr" rid="B2">2</xref>].</p><p><italic>Halomonas</italic>, the largest genus of the family <italic>Halomonadaceae</italic>, can be found in most saline environments, including marine environments, salterns, saline lakes and soils, as well as salty foods, etc. [<xref ref-type="bibr" rid="B5">5</xref>,<xref ref-type="bibr" rid="B6">6</xref>]. <italic>Halomonas zincidurans</italic> strain B6<sup>T</sup>, a moderately halophilic bacterium, was isolated from a deep-sea sediment from the South Atlantic Mid-Ocean Ridge [<xref ref-type="bibr" rid="B5">5</xref>]. The strain was able to grow in medium containing high concentrations of heavy metals, especially Zn<sup>2+</sup> ion, which is not detected in the reference strains and other moderately halophiles [<xref ref-type="bibr" rid="B5">5</xref>,<xref ref-type="bibr" rid="B7">7</xref>]. Therefore, the novel isolate was named as <italic>H. zincidurans</italic> due to its particular resistance to zinc ion [<xref ref-type="bibr" rid="B5">5</xref>]. Here, we present a summary classification and a set of features of <italic>H. zincidurans</italic> strain B6<sup>T</sup>, together with the description of the genomic sequencing and annotation.</p></sec><sec><title>Organism information</title><p>A deep-sea sediment sample, TVG10, was collected from the South Atlantic Mid-Ocean Ridge (Table <xref ref-type="table" rid="T1">1</xref>). There were many small hard orange red-colored lumps mixed in the sediment sample, which might be the particles containing ferric oxide and diffusing with hydrothermal plumes [<xref ref-type="bibr" rid="B8">8</xref>]. Not surprisingly, the concentrations of heavy metals in sample TVG10 were much higher than those in the samples collected from deep-sea seamount sediment [<xref ref-type="bibr" rid="B9">9</xref>], offshore sediment [<xref ref-type="bibr" rid="B10">10</xref>] and continental crust [<xref ref-type="bibr" rid="B11">11</xref>] (Additional file <xref ref-type="supplementary-material" rid="S1">1</xref>: Table S1), including Fe (98.99 mg/g), Mn (42.48 mg/g), Cu (0.839 mg/g), Ni (0.338 mg/g), Zn (0.285 mg/g), Cr (0.195 mg/g) and Co (0.064 mg/g). With consideration of the heavy metal rich environment, marine broth 2216 medium (MB, BD) containing 20 mM Mn<sup>2+</sup> was used to isolate heavy metal resistant strains. Subsequently a strain named B6<sup>T</sup> was obtained [<xref ref-type="bibr" rid="B5">5</xref>].</p><table-wrap position="float" id="T1"><label>Table 1</label><caption><p><bold>Classification and general features of </bold><bold><italic>H. zincidurans </italic></bold><bold>B6</bold><sup><bold>T </bold></sup><bold>according to the MIGS recommendations </bold>[<xref ref-type="bibr" rid="B12">12</xref>]</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="left"></col><col align="left"></col><col align="left"></col></colgroup><thead valign="top"><tr><th align="left"><bold>MIGS ID</bold></th><th align="left"><bold>Property</bold></th><th align="left"><bold>Term</bold></th><th align="left"><bold>Evidence code</bold><sup><bold>a</bold></sup></th></tr></thead><tbody valign="top"><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Current classification<hr></hr></td><td align="left" valign="bottom">Domain <italic>Bacteria</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B13">13</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Phylum <italic>Proteobacteria</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B14">14</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Class <italic>Gammaproteobacteria</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B16">16</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Order <italic>Oceanospirillales</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B17">17</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Family <italic>Halomonadaceae</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B18">18</xref>]–[<xref ref-type="bibr" rid="B22">22</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Genus <italic>Halomonas</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B22">22</xref>]–[<xref ref-type="bibr" rid="B24">24</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Species <italic>Halomonas zincidurans</italic><hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Type strain B6<sup>T</sup> = CGMCC 1.12450<sup>T</sup> = JCM 18472<sup>T</sup><hr></hr></td><td align="left" valign="bottom"> <hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Gram stain<hr></hr></td><td align="left" valign="bottom">Negative<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Cell shape<hr></hr></td><td align="left" valign="bottom">Rod<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Motility<hr></hr></td><td align="left" valign="bottom">Motile<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Sporulation<hr></hr></td><td align="left" valign="bottom">Nonsporulating<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Temperature range<hr></hr></td><td align="left" valign="bottom">4-37°C<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Optimum temperature<hr></hr></td><td align="left" valign="bottom">35°C<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">pH range; Optimum<hr></hr></td><td align="left" valign="bottom">5.0-8.5; 7.0<hr></hr></td><td align="left" valign="bottom"> <hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Carbon source<hr></hr></td><td align="left" valign="bottom">Adonitol, L-arabinose, cellobiose, ethanol, D-fructose, D-glucose, glycerol, maltose, mannitol, D-mannose, D-ribose, D-salicin, D-sorbitol, starch, D-xylose, acetate, citrate, D-gluconate, propionate, pyruvate, succinate, L-alanine, L-arginine, glycine, L-glutamate, L-lysine, L-ornithine and L-serine<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-6<hr></hr></td><td align="left" valign="bottom">Habitat<hr></hr></td><td align="left" valign="bottom">Deep-sea sediment<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-6.3<hr></hr></td><td align="left" valign="bottom">Salinity<hr></hr></td><td align="left" valign="bottom">Moderately halophilic, 0.5-15% NaCl<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-22<hr></hr></td><td align="left" valign="bottom">Oxygen<hr></hr></td><td align="left" valign="bottom">Strictly aerobic<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-15<hr></hr></td><td align="left" valign="bottom">Biotic relationship<hr></hr></td><td align="left" valign="bottom">Free-living<hr></hr></td><td align="left" valign="bottom">NAS<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-14<hr></hr></td><td align="left" valign="bottom">Pathogenicity<hr></hr></td><td align="left" valign="bottom">Not reported<hr></hr></td><td align="left" valign="bottom"> <hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-4<hr></hr></td><td align="left" valign="bottom">Geographic location<hr></hr></td><td align="left" valign="bottom">South Atlantic Ocean<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-5<hr></hr></td><td align="left" valign="bottom">Sample collection time<hr></hr></td><td align="left" valign="bottom">Feb 20, 2012<hr></hr></td><td align="left" valign="bottom">NAS<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-4.1<hr></hr></td><td align="left" valign="bottom">Latitude<hr></hr></td><td align="left" valign="bottom">13.60° S<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-4.2<hr></hr></td><td align="left" valign="bottom">Longitude<hr></hr></td><td align="left" valign="bottom">14.52° W<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-4.3<hr></hr></td><td align="left" valign="bottom">Depth<hr></hr></td><td align="left" valign="bottom">2950 m<hr></hr></td><td align="left" valign="bottom">TAS [<xref ref-type="bibr" rid="B5">5</xref>]<hr></hr></td></tr><tr><td align="left">MIGS-4.4</td><td align="left">Altitude</td><td align="left">-2950 m</td><td align="left">TAS [<xref ref-type="bibr" rid="B5">5</xref>]</td></tr></tbody></table><table-wrap-foot><p>Evidence codes - TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [<xref ref-type="bibr" rid="B25">25</xref>].</p></table-wrap-foot></table-wrap><p><italic>H. zincidurans</italic> strain B6<sup>T</sup> is a Gram-stained negative, rod-shaped (Figure <xref ref-type="fig" rid="F1">1</xref>), moderately halophilic bacterium growing at 0.5-15% (w/v) NaCl (Table <xref ref-type="table" rid="T1">1</xref>). Strain B6<sup>T</sup> exhibited the highest 16S rRNA gene sequence similarity with <italic>H. xinjiangensis</italic> (96.1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B6<sup>T</sup> and <italic>H. xinjiangensis</italic> clustered together in a distinct branch within the genus <italic>Halomonas</italic> with a high bootstrap value (Figure <xref ref-type="fig" rid="F2">2</xref>). Strain B6<sup>T</sup> was able to resist high concentrations of heavy metals in liquid HM medium, including Mn<sup>2+</sup> (200 mM), Co<sup>2+</sup> (1.0 mM), Cu<sup>2+</sup> (2.5 mM) and Zn<sup>2+</sup> (14 mM). Its resistance to Zn<sup>2+</sup> could be much higher (30 mM) when incubated on marine agar 2216 medium (MA, BD) [<xref ref-type="bibr" rid="B5">5</xref>], comparing to only 1 mM Zn<sup>2+</sup> resisted by <italic>H. xinjiangensis</italic> TRM0175<sup>T</sup>. And the maximum zinc resistance concentration for 250 moderately halophilic bacteria, reported by Nieto <italic>et al</italic>., was only 2.5 mM [<xref ref-type="bibr" rid="B7">7</xref>]. Therefore, <italic>H. zincidurans</italic> strain B6<sup>T</sup> is of significant interest due to its prominent resistance to zinc.</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Micrograph of </bold><bold><italic>H. zincidurans </italic></bold><bold>strain B6</bold><sup><bold>T </bold></sup><bold>obtained by scanning electron microscopy (S260; Cambridge).</bold></p></caption><graphic xlink:href="1944-3277-9-30-1"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Phylogenetic tree highlighting the position of </bold><bold><italic>H. zincidurans </italic></bold><bold>strain B6</bold><sup><bold>T </bold></sup><bold>relative to phylogenetically closely related type strains within the family Halomonadaceae.</bold> The sequences were aligned using Clustal W [<xref ref-type="bibr" rid="B26">26</xref>], and the neighbor-joining tree [<xref ref-type="bibr" rid="B27">27</xref>] was constructed based on kimura 2-parameter distance model [<xref ref-type="bibr" rid="B28">28</xref>] by using MEGA5 [<xref ref-type="bibr" rid="B29">29</xref>]. Bootstrap values above 60% are shown obtained from 1,000 bootstrap replications. Bar, 0.05 substitutions per nucleotide position. The corresponding GenBank accession numbers are displayed in parentheses.</p></caption><graphic xlink:href="1944-3277-9-30-2"></graphic></fig></sec><sec><title>Genome sequencing information</title><sec><title>Genome project history</title><p>The next-generation shotgun-sequencing and quality assurance was performed at the Beijing Genome Institute (BGI, Shenzhen). The gap closure and annotation processes were performed by the authors. The Whole Genome Shotgun project of <italic>H. zincidurans</italic> strain B6<sup>T</sup> has been deposited at DDBJ/EMBL/GenBank under the accession JNCK00000000. The version described in this paper is version JNCK01000000. Table <xref ref-type="table" rid="T2">2</xref> presents the project information and its association with MIGS version 2.0 compliance [<xref ref-type="bibr" rid="B12">12</xref>].</p><table-wrap position="float" id="T2"><label>Table 2</label><caption><p>Project information</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="left"></col><col align="left"></col></colgroup><thead valign="top"><tr><th align="left"><bold>MIGS ID</bold></th><th align="left"><bold>Property</bold></th><th align="left"><bold>Term</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="bottom">MIGS-31<hr></hr></td><td align="left" valign="bottom">Finishing quality<hr></hr></td><td align="left" valign="bottom">High-quality draft<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-28<hr></hr></td><td align="left" valign="bottom">Libraries used<hr></hr></td><td align="left" valign="bottom">One pair-end 494 bp library and one pair-end 2,586 bp library<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-29<hr></hr></td><td align="left" valign="bottom">Sequencing platforms<hr></hr></td><td align="left" valign="bottom">Illumina HiSeq 2000<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-31.2<hr></hr></td><td align="left" valign="bottom">Fold coverage<hr></hr></td><td align="left" valign="bottom">120 × (494 bp library) and 90 × (2,586 bp library)<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-30<hr></hr></td><td align="left" valign="bottom">Assemblers<hr></hr></td><td align="left" valign="bottom">SOAP<italic>denovo</italic>[<xref ref-type="bibr" rid="B30">30</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom">MIGS-32<hr></hr></td><td align="left" valign="bottom">Gene calling method<hr></hr></td><td align="left" valign="bottom">Glimmer v3.02 [<xref ref-type="bibr" rid="B31">31</xref>]<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Locus Tag<hr></hr></td><td align="left" valign="bottom">HALZIN<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Genbank ID<hr></hr></td><td align="left" valign="bottom">JNCK00000000<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Genbank Date of Release<hr></hr></td><td align="left" valign="bottom">July 21, 2014<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">GOLD ID<hr></hr></td><td align="left" valign="bottom">Gi0069861<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">BIOPROJECT<hr></hr></td><td align="left" valign="bottom">PRJNA234075<hr></hr></td></tr><tr><td align="left" valign="bottom"> <hr></hr></td><td align="left" valign="bottom">Project relevance<hr></hr></td><td align="left" valign="bottom">Type strain, environmental, heavy metal resistance<hr></hr></td></tr><tr><td align="left">MIGS-13</td><td align="left">Source Material Identifier</td><td align="left">CGMCC 1.12450, JCM 18472</td></tr></tbody></table></table-wrap></sec><sec><title>Growth conditions and DNA isolation</title><p><italic>H. zincidurans</italic> strain B6<sup>T</sup> was aerobically cultivated in MB medium at 30°C. Total genomic DNA was extracted using the method described by Marmur [<xref ref-type="bibr" rid="B32">32</xref>]. The quality and quantity of the genomic DNA was determined by 0.6% agarose gel electrophoresis with <italic>λ</italic>-Hind III digest DNA marker (TaKaRa, Dalian, China) and by a Qubit® fluorometer (Invitrogen, CA, USA) with Qubit dsDNA BR Assay kit (Invitrogen, CA, USA). About 350 μg DNA with a concentration of 450 ng/μl was obtained.</p></sec><sec><title>Genome sequencing and assembly</title><p>Whole-genome shotgun DNA sequencing of <italic>H. zincidurans</italic> strain B6<sup>T</sup> was performed using Solexa paired-end sequencing technology (HiSeq2000 system, Illumina, USA) [<xref ref-type="bibr" rid="B33">33</xref>]. Two libraries with insert size 494 bp and 2,586 bp were constructed and a total of 519 Mb and 416 Mb raw data were produced before filtering. After removing the adapter, duplicated reads and short inserts from the data of large library, there remained 433 Mb (~120-folds genome coverage) and 328 Mb (~90-folds genome coverage) clean data from the small and large libraries for assembling, respectively. Then these sequences were assembled into 15 contigs using the SOAP<italic>denovo</italic> v.1.05 [<xref ref-type="bibr" rid="B30">30</xref>], the contig N50 length of which was 1,864,365 bp. PCR primers for gap closure were designed by Primer Premier v.5. PCR reactions were performed with PrimeSTAR HS Polymerase (TaKaRa, Dalian, China) and the amplicons were sequenced using Sanger and primer walking technologies. The sequenced fragments were subsequently assembled with the contigs using SeqMan of the Lasergene package (DNAstar, Madison, WI) into 2 contigs.</p></sec><sec><title>Genome annotation</title><p>The whole genomic tRNAs were identified using tRNAscan-SE v.1.21 [<xref ref-type="bibr" rid="B34">34</xref>] with bacterial model, and rRNAs were found by RNAmmer v.1.2 Server [<xref ref-type="bibr" rid="B35">35</xref>]. ORFs were predicted using Glimmer v.3.0 [<xref ref-type="bibr" rid="B31">31</xref>]. The predicted ORFs were translated and analyzed using the NCBI nonredundant, Swiss-Prot [<xref ref-type="bibr" rid="B36">36</xref>] and COG [<xref ref-type="bibr" rid="B37">37</xref>] databases, as well as RAST server online [<xref ref-type="bibr" rid="B38">38</xref>] for genome annotation. KAAS [<xref ref-type="bibr" rid="B39">39</xref>] was used to assign the predict proteins into KEGG pathway [<xref ref-type="bibr" rid="B40">40</xref>] with BBH method. Genes with signal peptides and transmembrane helices were predicted using TMHMM server v.2.0 [<xref ref-type="bibr" rid="B41">41</xref>] and SignalP server v.4.1 [<xref ref-type="bibr" rid="B42">42</xref>], respectively. The G+C content, G+C content at the third-codon position and RSCU were calculated by CodonW v.1.4.4.</p></sec></sec><sec><title>Genome properties</title><p>The genome was assembled into 2 contigs, one with a size of 3,546,937 bp and the other with 7,823 bp (Table <xref ref-type="table" rid="T3">3</xref>). The G+C content determined based on the total 3,554,760 bp sequences was 66.41%. A total of 3,392 genes were predicted, including 3,325 protein-coding genes, 61 tRNA genes and two copies of 16S-23S-5S rRNA gene operons (Table <xref ref-type="table" rid="T4">4</xref> and Figure <xref ref-type="fig" rid="F2">2</xref>). Among the protein coding genes, 2,848 were assigned to putative functions, and the remaining was annotated as hypothetical proteins. In total, 1,938 and 442 protein coding genes were assigned to KEGG and subsystems, respectively. The detailed properties and the statistics of the genome as well as the distribution of genes into COG functional categories are summarized in Tables <xref ref-type="table" rid="T3">3</xref>, <xref ref-type="table" rid="T4">4</xref> and <xref ref-type="table" rid="T5">5</xref>, Figure <xref ref-type="fig" rid="F3">3</xref> and Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>: Table S2.</p><table-wrap position="float" id="T3"><label>Table 3</label><caption><p>Summary of genome: two contigs</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="top"><tr><th align="left"><bold>Label</bold></th><th align="center"><bold>Size (Mb)</bold></th><th align="center"><bold>Topology</bold></th><th align="center"><bold>INSDC identifier</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="bottom">Contig 1<hr></hr></td><td align="center" valign="bottom">3.546937<hr></hr></td><td align="center" valign="bottom">Linear<hr></hr></td><td align="center" valign="bottom">JNCK01000001.1<hr></hr></td></tr><tr><td align="left">Contig 2</td><td align="center">0.007823</td><td align="center">Linear</td><td align="center">JNCK01000002.1</td></tr></tbody></table></table-wrap><table-wrap position="float" id="T4"><label>Table 4</label><caption><p>Nucleotide content and gene count levels of the genome</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="right"></col><col align="right"></col></colgroup><thead valign="top"><tr><th align="left" valign="bottom"><bold>Attribute</bold><hr></hr></th><th align="right" valign="bottom"> <hr></hr></th><th align="center" valign="bottom"><bold>Genome (total)</bold><hr></hr></th></tr><tr><th align="left"> </th><th align="right"><bold>Value</bold></th><th align="right"><bold>% of total</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="bottom">Genome size (bp)<hr></hr></td><td align="right" valign="bottom">3,554,760<hr></hr></td><td align="right" valign="bottom">-<hr></hr></td></tr><tr><td align="left" valign="bottom">DNA coding (bp)<hr></hr></td><td align="right" valign="bottom">3,153,982<hr></hr></td><td align="right" valign="bottom">88.73<hr></hr></td></tr><tr><td align="left" valign="bottom">DNA G+C (bp)<hr></hr></td><td align="right" valign="bottom">2,289,453<hr></hr></td><td align="right" valign="bottom">66.41<hr></hr></td></tr><tr><td align="left" valign="bottom">DNA scaffolds<hr></hr></td><td align="right" valign="bottom">2<hr></hr></td><td align="right" valign="bottom">-<hr></hr></td></tr><tr><td align="left" valign="bottom">Total genes<hr></hr></td><td align="right" valign="bottom">3,392<hr></hr></td><td align="right" valign="bottom">-<hr></hr></td></tr><tr><td align="left" valign="bottom">Protein coding genes<hr></hr></td><td align="right" valign="bottom">3,325<hr></hr></td><td align="right" valign="bottom">98.02<hr></hr></td></tr><tr><td align="left" valign="bottom">RNA genes<hr></hr></td><td align="right" valign="bottom">67<hr></hr></td><td align="right" valign="bottom">1.98<hr></hr></td></tr><tr><td align="left" valign="bottom">Genes with function prediction<hr></hr></td><td align="right" valign="bottom">2,916<hr></hr></td><td align="right" valign="bottom">85.97<hr></hr></td></tr><tr><td align="left" valign="bottom">Genes assigned to COGs<hr></hr></td><td align="right" valign="bottom">2,764<hr></hr></td><td align="right" valign="bottom">81.49<hr></hr></td></tr><tr><td align="left" valign="bottom">1 or more conserved domains<hr></hr></td><td align="right" valign="bottom">2,764<hr></hr></td><td align="right" valign="bottom">81.49<hr></hr></td></tr><tr><td align="left" valign="bottom">2 or more conserved domains<hr></hr></td><td align="right" valign="bottom">329<hr></hr></td><td align="right" valign="bottom">9.70<hr></hr></td></tr><tr><td align="left" valign="bottom">3 or more conserved domains<hr></hr></td><td align="right" valign="bottom">74<hr></hr></td><td align="right" valign="bottom">2.18<hr></hr></td></tr><tr><td align="left" valign="bottom">4 or more conserved domains<hr></hr></td><td align="right" valign="bottom">23<hr></hr></td><td align="right" valign="bottom">0.68<hr></hr></td></tr><tr><td align="left" valign="bottom">Genes with Pfam domains<hr></hr></td><td align="right" valign="bottom">2,188<hr></hr></td><td align="right" valign="bottom">64.50<hr></hr></td></tr><tr><td align="left" valign="bottom">Genes with signal peptides<hr></hr></td><td align="right" valign="bottom">180<hr></hr></td><td align="right" valign="bottom">5.31<hr></hr></td></tr><tr><td align="left" valign="bottom">Genes with transmembrane helices<hr></hr></td><td align="right" valign="bottom">697<hr></hr></td><td align="right" valign="bottom">20.55<hr></hr></td></tr><tr><td align="left">CRISPR repeats</td><td align="right">1</td><td align="right">-</td></tr></tbody></table></table-wrap><table-wrap position="float" id="T5"><label>Table 5</label><caption><p>Number of genes associated with the 25 general COG functional categories</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="center"></col><col align="left"></col><col align="left"></col><col align="left"></col></colgroup><thead valign="top"><tr><th align="center"><bold>Code</bold></th><th align="left"><bold>Value</bold></th><th align="left"><bold>% of total</bold></th><th align="left"><bold>Description</bold></th></tr></thead><tbody valign="top"><tr><td align="center" valign="bottom">J<hr></hr></td><td align="left" valign="bottom">164<hr></hr></td><td align="left" valign="bottom">5.14<hr></hr></td><td align="left" valign="bottom">Translation<hr></hr></td></tr><tr><td align="center" valign="bottom">A<hr></hr></td><td align="left" valign="bottom">1<hr></hr></td><td align="left" valign="bottom">0.03<hr></hr></td><td align="left" valign="bottom">RNA processing and modification<hr></hr></td></tr><tr><td align="center" valign="bottom">K<hr></hr></td><td align="left" valign="bottom">230<hr></hr></td><td align="left" valign="bottom">7.21<hr></hr></td><td align="left" valign="bottom">Transcription<hr></hr></td></tr><tr><td align="center" valign="bottom">L<hr></hr></td><td align="left" valign="bottom">188<hr></hr></td><td align="left" valign="bottom">5.89<hr></hr></td><td align="left" valign="bottom">Replication, recombination and repair<hr></hr></td></tr><tr><td align="center" valign="bottom">B<hr></hr></td><td align="left" valign="bottom">4<hr></hr></td><td align="left" valign="bottom">0.13<hr></hr></td><td align="left" valign="bottom">Chromatin structure and dynamics<hr></hr></td></tr><tr><td align="center" valign="bottom">D<hr></hr></td><td align="left" valign="bottom">32<hr></hr></td><td align="left" valign="bottom">1.00<hr></hr></td><td align="left" valign="bottom">Cell cycle control, mitosis and meiosis<hr></hr></td></tr><tr><td align="center" valign="bottom">Y<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Nuclear structure<hr></hr></td></tr><tr><td align="center" valign="bottom">V<hr></hr></td><td align="left" valign="bottom">33<hr></hr></td><td align="left" valign="bottom">1.03<hr></hr></td><td align="left" valign="bottom">Defense mechanisms<hr></hr></td></tr><tr><td align="center" valign="bottom">T<hr></hr></td><td align="left" valign="bottom">127<hr></hr></td><td align="left" valign="bottom">3.98<hr></hr></td><td align="left" valign="bottom">Signal transduction mechanisms<hr></hr></td></tr><tr><td align="center" valign="bottom">M<hr></hr></td><td align="left" valign="bottom">182<hr></hr></td><td align="left" valign="bottom">5.71<hr></hr></td><td align="left" valign="bottom">Cell wall/membrane biogenesis<hr></hr></td></tr><tr><td align="center" valign="bottom">N<hr></hr></td><td align="left" valign="bottom">64<hr></hr></td><td align="left" valign="bottom">2.01<hr></hr></td><td align="left" valign="bottom">Cell motility<hr></hr></td></tr><tr><td align="center" valign="bottom">Z<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Cytoskeleton<hr></hr></td></tr><tr><td align="center" valign="bottom">W<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Extracellular structures<hr></hr></td></tr><tr><td align="center" valign="bottom">U<hr></hr></td><td align="left" valign="bottom">62<hr></hr></td><td align="left" valign="bottom">1.94<hr></hr></td><td align="left" valign="bottom">Intracellular trafficking and secretion<hr></hr></td></tr><tr><td align="center" valign="bottom">O<hr></hr></td><td align="left" valign="bottom">109<hr></hr></td><td align="left" valign="bottom">3.42<hr></hr></td><td align="left" valign="bottom">Posttranslational modification, protein turnover, chaperones<hr></hr></td></tr><tr><td align="center" valign="bottom">C<hr></hr></td><td align="left" valign="bottom">215<hr></hr></td><td align="left" valign="bottom">6.74<hr></hr></td><td align="left" valign="bottom">Energy production and conversion<hr></hr></td></tr><tr><td align="center" valign="bottom">G<hr></hr></td><td align="left" valign="bottom">216<hr></hr></td><td align="left" valign="bottom">6.77<hr></hr></td><td align="left" valign="bottom">Carbohydrate transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">E<hr></hr></td><td align="left" valign="bottom">325<hr></hr></td><td align="left" valign="bottom">10.19<hr></hr></td><td align="left" valign="bottom">Amino acid transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">F<hr></hr></td><td align="left" valign="bottom">76<hr></hr></td><td align="left" valign="bottom">2.38<hr></hr></td><td align="left" valign="bottom">Nucleotide transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">H<hr></hr></td><td align="left" valign="bottom">145<hr></hr></td><td align="left" valign="bottom">4.55<hr></hr></td><td align="left" valign="bottom">Coenzyme transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">I<hr></hr></td><td align="left" valign="bottom">118<hr></hr></td><td align="left" valign="bottom">3.70<hr></hr></td><td align="left" valign="bottom">Lipid transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">P<hr></hr></td><td align="left" valign="bottom">171<hr></hr></td><td align="left" valign="bottom">5.36<hr></hr></td><td align="left" valign="bottom">Inorganic ion transport and metabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">Q<hr></hr></td><td align="left" valign="bottom">108<hr></hr></td><td align="left" valign="bottom">3.39<hr></hr></td><td align="left" valign="bottom">Secondary metabolites biosynthesis, transport and catabolism<hr></hr></td></tr><tr><td align="center" valign="bottom">R<hr></hr></td><td align="left" valign="bottom">391<hr></hr></td><td align="left" valign="bottom">12.26<hr></hr></td><td align="left" valign="bottom">General function prediction only<hr></hr></td></tr><tr><td align="center" valign="bottom">S<hr></hr></td><td align="left" valign="bottom">229<hr></hr></td><td align="left" valign="bottom">7.18<hr></hr></td><td align="left" valign="bottom">Function unknown<hr></hr></td></tr><tr><td align="center">-</td><td align="left">628</td><td align="left">18.51</td><td align="left">Not in COGs</td></tr></tbody></table></table-wrap><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>Circular map of the chromosome of </bold><bold><italic>H. zincidurans </italic></bold><bold>strain B6</bold><sup><bold>T</bold></sup><bold>.</bold> Labeling from the outside to the inside circle: ORFs on the forward strand (colored by COG categories), ORFs on the reverse strand (colored by COG categories), RNA genes (tRNAs red, rRNAs blue), G+C content (peaks out/inside the circle indicate values higher or lower than the average G+C content, respectively), GC skew (calculated as (G-C)/(G+C), green/purple peaks out/inside the circle indicates values higher or lower than 1, respectively).</p></caption><graphic xlink:href="1944-3277-9-30-3"></graphic></fig></sec><sec><title>Insights into the genome</title><p>The genome of <italic>H. zincidurans</italic> strain B6<sup>T</sup> contains 31 genes related to heavy metal resistance, especially to zinc resistance (Table <xref ref-type="table" rid="T6">6</xref>). Zinc is an essential but also toxic metal for living being [<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B43">43</xref>]. The concentration of zinc inside bacterial cells is maintained by importing limitation, efflux, accumulation and sequestration [<xref ref-type="bibr" rid="B44">44</xref>,<xref ref-type="bibr" rid="B45">45</xref>]. <italic>H. zincidurans</italic> strain B6<sup>T</sup> possesses four heavy metal translocating P-type ATPases (HALZIN_733, HALZIN_1240, HALZIN_2196 and HALZIN_2262), which may participate in the transport of Zn<sup>2+</sup>, Mn<sup>2+</sup>, Cu<sup>2+</sup>, Cd<sup>2+</sup>, Pb<sup>2+</sup>, Ag + and Hg<sup>2+</sup> against the concentration gradient to the periplasm [<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B44">44</xref>]. Especially the two ZntA P-type ATPases (HALZIN_733 and HALZIN_2196) may mediate resistance to Zn<sup>2+</sup>, Cd<sup>2+</sup> and Pb<sup>2+</sup>[<xref ref-type="bibr" rid="B46">46</xref>,<xref ref-type="bibr" rid="B47">47</xref>]. Zn<sup>2+</sup>, Co<sup>2+</sup>, Cu<sup>2+</sup>, Cd<sup>2+</sup> and Ni<sup>2+</sup> are able to be transported by RND family efflux transporter protein (HALZIN_54, HALZIN_1411, HALZIN_2047, HALZIN_2208 and HALZIN_2209) from both the cytoplasm and the periplasm to outside [<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B44">44</xref>]. Usually the P-type ATPases are regulated by MerR family regulators responding to the intracellular heavy metal concentration [<xref ref-type="bibr" rid="B44">44</xref>,<xref ref-type="bibr" rid="B48">48</xref>,<xref ref-type="bibr" rid="B49">49</xref>]. Six analogues of MerR family regulators (HALZIN_399, HALZIN_922, HALZIN_2261, HALZIN_2264, HALZIN_2469 and HALZIN_2675) were found in the genome of <italic>H. zincidurans</italic> strain B6<sup>T</sup>. Additionally, a zinc uptake regulation protein ZUR (HALZIN_1413), which is a repressor regulator during zinc uptake, is also detected [<xref ref-type="bibr" rid="B44">44</xref>,<xref ref-type="bibr" rid="B50">50</xref>]. The presence of these genes is accordance with zinc resistance phenotype of <italic>H. zincidurans</italic> strain B6<sup>T</sup>.</p><table-wrap position="float" id="T6"><label>Table 6</label><caption><p>Description of the genes related to heavy metal resistance</p></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="center"></col><col align="right"></col><col align="right"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="top"><tr><th rowspan="2" align="center" valign="top"><bold>Protein id</bold></th><th rowspan="2" align="right" valign="top"><bold>Position</bold></th><th rowspan="2" align="right" valign="top"><bold>Size/aa</bold></th><th rowspan="2" align="center" valign="top"><bold>Strand</bold></th><th rowspan="2" align="left" valign="top"><bold>Predicted function</bold></th><th colspan="4" align="center" valign="bottom"><bold>Closest relatives</bold><hr></hr></th></tr><tr><th align="left"><bold>Organism</bold></th><th align="left"><bold>Class</bold></th><th align="center"><bold>Identity</bold></th><th align="center"><bold>Accession no.</bold></th></tr></thead><tbody valign="top"><tr><td align="center" valign="bottom">HALZIN_54<hr></hr></td><td align="right" valign="bottom">48442-49500<hr></hr></td><td align="right" valign="bottom">352<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">RND family efflux transporter, MFP subunit<hr></hr></td><td align="left" valign="bottom"><italic>Idiomarina sediminum</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">44%<hr></hr></td><td align="center" valign="bottom">WP_026860724<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_399<hr></hr></td><td align="right" valign="bottom">433553-434005<hr></hr></td><td align="right" valign="bottom">150<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">MerR family Cd(II)/Pb(II)-responsive transcriptional regulator<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">75%<hr></hr></td><td align="center" valign="bottom">WP_019019418<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_733<hr></hr></td><td align="right" valign="bottom">778272-780812<hr></hr></td><td align="right" valign="bottom">846<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Heavy metal translocating P-type ATPase ZntA<hr></hr></td><td align="left" valign="bottom"><italic>Gracilimonas tropica</italic><hr></hr></td><td align="left" valign="bottom"><italic>Sphingobacteriia</italic><hr></hr></td><td align="center" valign="bottom">59%<hr></hr></td><td align="center" valign="bottom">WP_020403952<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_916<hr></hr></td><td align="right" valign="bottom">977118-976882<hr></hr></td><td align="right" valign="bottom">78<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Mercuric transport protein MerE<hr></hr></td><td align="left" valign="bottom"><italic>Burkholderia cepacia</italic><hr></hr></td><td align="left" valign="bottom"><italic>Betaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">99%<hr></hr></td><td align="center" valign="bottom">YP_006965885<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_917<hr></hr></td><td align="right" valign="bottom">977480-977115<hr></hr></td><td align="right" valign="bottom">121<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerD<hr></hr></td><td align="left" valign="bottom"><italic>Pseudomonas putida</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">98%<hr></hr></td><td align="center" valign="bottom">WP_012806008<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_918<hr></hr></td><td align="right" valign="bottom">978239-977592<hr></hr></td><td align="right" valign="bottom">215<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Alkylmercury lyase MerB<hr></hr></td><td align="left" valign="bottom"><italic>Paraglaciecola polaris</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">84%<hr></hr></td><td align="center" valign="bottom">WP_007106069<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_919<hr></hr></td><td align="right" valign="bottom">979028-978390<hr></hr></td><td align="right" valign="bottom">212<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Alkylmercury lyase MerB<hr></hr></td><td align="left" valign="bottom"><italic>Paraglaciecola polaris</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">94%<hr></hr></td><td align="center" valign="bottom">WP_007106069<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_920<hr></hr></td><td align="right" valign="bottom">979808-979179<hr></hr></td><td align="right" valign="bottom">209<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Alkylmercury lyase MerB<hr></hr></td><td align="left" valign="bottom"><italic>Paraglaciecola polaris</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">90%<hr></hr></td><td align="center" valign="bottom">WP_007106069<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_922<hr></hr></td><td align="right" valign="bottom">980118-980540<hr></hr></td><td align="right" valign="bottom">140<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerR<hr></hr></td><td align="left" valign="bottom"><italic>Stenotrophomonas maltophilia</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">99%<hr></hr></td><td align="center" valign="bottom">WP_005413398<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_934<hr></hr></td><td align="right" valign="bottom">994405-993521<hr></hr></td><td align="right" valign="bottom">294<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Magnesium and cobalt efflux protein CorC<hr></hr></td><td align="left" valign="bottom"><italic>Chromohalobacter salexigens</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">81%<hr></hr></td><td align="center" valign="bottom">WP_011507633<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_1240<hr></hr></td><td align="right" valign="bottom">1334217-1331998<hr></hr></td><td align="right" valign="bottom">739<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Heavy metal translocating P-type ATPase<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas</italic> sp.<hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">97%<hr></hr></td><td align="center" valign="bottom">WP_023004666<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_1392<hr></hr></td><td align="right" valign="bottom">1499237-1498659<hr></hr></td><td align="right" valign="bottom">192<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Superoxide dismutase<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas smyrnensis</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">85%<hr></hr></td><td align="center" valign="bottom">WP_016854901<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_1411<hr></hr></td><td align="right" valign="bottom">1521826-1522995<hr></hr></td><td align="right" valign="bottom">389<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">RND family efflux transporter, MFP subunit<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">76%<hr></hr></td><td align="center" valign="bottom">WP_019017686<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_1413<hr></hr></td><td align="right" valign="bottom">1526330-1526785<hr></hr></td><td align="right" valign="bottom">151<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Zinc uptake regulation protein ZUR<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">82%<hr></hr></td><td align="center" valign="bottom">WP_019017691<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2047<hr></hr></td><td align="right" valign="bottom">2179598-2182789<hr></hr></td><td align="right" valign="bottom">1063<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">RND family efflux transporter protein<hr></hr></td><td align="left" valign="bottom"><italic>Pseudoxanthomonas suwonensis</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">85%<hr></hr></td><td align="center" valign="bottom">WP_013535339<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2196<hr></hr></td><td align="right" valign="bottom">2338252-2335574<hr></hr></td><td align="right" valign="bottom">892<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Heavy metal translocating P-type ATPase ZntA<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">65%<hr></hr></td><td align="center" valign="bottom">WP_019020337<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2208<hr></hr></td><td align="right" valign="bottom">2355137-2351976<hr></hr></td><td align="right" valign="bottom">1053<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">RND family efflux transporter protein<hr></hr></td><td align="left" valign="bottom"><italic>Pseudomonas alcaligenes</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">58%<hr></hr></td><td align="center" valign="bottom">WP_021217164<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2209<hr></hr></td><td align="right" valign="bottom">2356423-2351976<hr></hr></td><td align="right" valign="bottom">428<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">RND family efflux transporter, MFP subunit<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">53%<hr></hr></td><td align="center" valign="bottom">WP_019020155<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2260<hr></hr></td><td align="right" valign="bottom">2411989-2410787<hr></hr></td><td align="right" valign="bottom">400<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Multicopper oxidase<hr></hr></td><td align="left" valign="bottom"><italic>Sphingopyxis baekryungensis</italic><hr></hr></td><td align="left" valign="bottom"><italic>Alphaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">55%<hr></hr></td><td align="center" valign="bottom">WP_022673021<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2261<hr></hr></td><td align="right" valign="bottom">2412630-2413034<hr></hr></td><td align="right" valign="bottom">134<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerR<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">90%<hr></hr></td><td align="center" valign="bottom">WP_019017365<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2262<hr></hr></td><td align="right" valign="bottom">2413107-2415596<hr></hr></td><td align="right" valign="bottom">829<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Heavy metal translocating P-type ATPase<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">92%<hr></hr></td><td align="center" valign="bottom">WP_019017357<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2264<hr></hr></td><td align="right" valign="bottom">2416527-2416976<hr></hr></td><td align="right" valign="bottom">149<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerR<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">89%<hr></hr></td><td align="center" valign="bottom">WP_026300314<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2268<hr></hr></td><td align="right" valign="bottom">2423176-2423622<hr></hr></td><td align="right" valign="bottom">148<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">CopG family transcriptional regulator<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">80%<hr></hr></td><td align="center" valign="bottom">WP_019017364<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2271<hr></hr></td><td align="right" valign="bottom">2424931-2425086<hr></hr></td><td align="right" valign="bottom">51<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Copper resistance protein CopC<hr></hr></td><td align="left" valign="bottom"><italic>Hyphomonas neptunium</italic><hr></hr></td><td align="left" valign="bottom"><italic>Alphaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">51%<hr></hr></td><td align="center" valign="bottom">WP_011646711<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2272<hr></hr></td><td align="right" valign="bottom">2425115-2425978<hr></hr></td><td align="right" valign="bottom">287<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Copper resistance protein CopD<hr></hr></td><td align="left" valign="bottom"><italic>Thialkalivibrio</italic> sp.<hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">43%<hr></hr></td><td align="center" valign="bottom">WP_018881395<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2469<hr></hr></td><td align="right" valign="bottom">2658088-2657690<hr></hr></td><td align="right" valign="bottom">132<hr></hr></td><td align="center" valign="bottom">-<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerR<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">90%<hr></hr></td><td align="center" valign="bottom">WP_019020805<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2470<hr></hr></td><td align="right" valign="bottom">2658244-2658588<hr></hr></td><td align="right" valign="bottom">114<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Mercuric transport protein MerT<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">78%<hr></hr></td><td align="center" valign="bottom">WP_019020806<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2471<hr></hr></td><td align="right" valign="bottom">2658620-2658925<hr></hr></td><td align="right" valign="bottom">101<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Periplasmic mercury(+2) binding protein MerP<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">82%<hr></hr></td><td align="center" valign="bottom">WP_019020807<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2472<hr></hr></td><td align="right" valign="bottom">2658988-2660622<hr></hr></td><td align="right" valign="bottom">544<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Mercuric reductase, MerA family<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas lutea</italic><hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">93%<hr></hr></td><td align="center" valign="bottom">WP_019020808<hr></hr></td></tr><tr><td align="center" valign="bottom">HALZIN_2675<hr></hr></td><td align="right" valign="bottom">2872087-2872584<hr></hr></td><td align="right" valign="bottom">165<hr></hr></td><td align="center" valign="bottom">+<hr></hr></td><td align="left" valign="bottom">Transcriptional regulator MerR<hr></hr></td><td align="left" valign="bottom"><italic>Halomonas</italic> sp.<hr></hr></td><td align="left" valign="bottom"><italic>Gammaproteobacteria</italic><hr></hr></td><td align="center" valign="bottom">66%<hr></hr></td><td align="center" valign="bottom">WP_023005510<hr></hr></td></tr><tr><td align="center">HALZIN_3265</td><td align="right">3489632-3489021</td><td align="right">203</td><td align="center">-</td><td align="left">Superoxide dismutase</td><td align="left"><italic>Halomonas lutea</italic></td><td align="left"><italic>Gammaproteobacteria</italic></td><td align="center">74%</td><td align="center">WP_019019731</td></tr></tbody></table></table-wrap><p>Among the 31 ORFs related to heavy metal resistance, it is noteworthy of two <italic>mer</italic>-operons. One <italic>mer</italic>-operon encodes a mercuric transport protein (MerE, HALZIN_916) for organic mercury uptake [<xref ref-type="bibr" rid="B51">51</xref>], a transcriptional regulator (MerD, HALZIN_917), three alkylmercury lyases (MerB, HALZIN_918-920) catalyzing organomercurials yielding Hg<sup>2+</sup>[<xref ref-type="bibr" rid="B52">52</xref>] and a transcriptional regulator (MerR, HALZIN_922). The other one encodes a transcriptional regulator (MerR, HALZIN_2469), two mercuric transport proteins (MerT and MerP, HALZIN_2470-2471) for inorganic mercury uptake [<xref ref-type="bibr" rid="B51">51</xref>] and a mercuric reductase (MerA, HALZIN_2472) catalyzing Hg<sup>2+</sup> to Hg<sup>0</sup>[<xref ref-type="bibr" rid="B53">53</xref>]. According to the genomic data, <italic>H. zincidurans</italic> strain B6<sup>T</sup> is able to survive in both inorganic and organic mercury environments. Interestingly, the four ORFs of the inorganic <italic>mer</italic>-operon showed the highest sequence identities to those of <italic>Halomonas lutea</italic>. Nevertheless, all the six ORFs of the organic <italic>mer</italic>-operon did not show the highest sequence identities to those of the genus <italic>Halomonas</italic>, but to the genera <italic>Burkholderia</italic>, <italic>Pseudomonas</italic>, <italic>Gladiecola</italic> and <italic>Stenotrophomonas</italic>, which indicates that the organic <italic>mer</italic>-operon might be acquired by HGT. Of special interest are the three alkylmercury lyases (MerB, HALZIN_918-920), which had obvious differences between the G+C content (56.6%; 57.1, 56.6 and 56.0% for these three gene sequences, respectively) as well as the G+C content at the third-codon positions (60.3%; 60.4, 61.0 and 59.4% for these three gene sequences, respectively) and those of the total protein-coding genes (65.4 and 82.8%, respectively). Besides, the RSCUs of nearly half of the 59 codons used by the three genes (23, 27 and 26 codons for HALZIN_918-920, respectively) change more than 2 folds, compared with those used by total protein-coding genes. 13 of the 31 ORFs (41.9%) were not related to <italic>Halomonadaceae</italic> genes according to the gene sequence similarity analysis, 9 of the 13 ORFs had RSCU change larger than 2 folds in more than 25% codons. These results indicated the existence of HGT events among the heavy metal resistance-related genes. Thus, HGT events might be an important way for <italic>H. zincidurans</italic> strain B6<sup>T</sup> to acquire heavy metal resistant ability and to adapt to the heavy metal rich environment.</p></sec><sec sec-type="conclusions"><title>Conclusion</title><p>The draft genome sequence of the heavy metal resistant bacteria <italic>H. zincidurans</italic> strain B6<sup>T</sup> isolated from the South Atlantic Mid-Ocean Ridge provide an insight into the genomic basis of its heavy metal resistance ability. And HGT may play an important role in its adaption to the heavy metal rich environment. On the basis of analysis and characterization of genome, <italic>H. zincidurans</italic> strain B6<sup>T</sup> might be resistant more kinds of heavy metal than we tested, such as Hg<sup>2+</sup>, Cd<sup>2+</sup>, Pb<sup>2+</sup>, Ni<sup>2+</sup> and Ag<sup>+</sup>, etc. And it may have the potential for the bioremediation of multi-metal-contaminated environments. In addition, further analysis will be performed to confirm its resistant ability to other heavy metals and determine the mechanism of heavy metal resistance that we don’t know yet.</p></sec><sec><title>Abbreviations</title><p>HGT: Horizontal gene transfer; RSCU: Relative synonymous codon usage.</p></sec><sec><title>Competing interests</title><p>The authors declare that they have no competing interests.</p></sec><sec><title>Authors’ contributions</title><p>YH designed and performed experiments, analyzed data and wrote the paper; ZL performed experiments; HC analyzed genome data; CW analyzed data; XX designed the experiments and wrote the paper. All authors read and approved the final manuscript.</p></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="S1"><caption><title>Additional file 1: Table S1</title><p>Concentrations of heavy metals in deep-sea sediment collected from the South Atlantic Mid-Ocean Ridge (1) and the sediments from the Central Pacific seamount (2), offshore sediment (3) and continental crust (4).</p></caption><media xlink:href="1944-3277-9-30-S1.doc"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S2"><caption><title>Additional file 2: Table S2</title><p>Associated MIGS record.</p></caption><media xlink:href="1944-3277-9-30-S2.doc"><caption><p>Click here for file</p></caption></media></supplementary-material></sec></body><back><sec><title>Acknowledgements</title><p>This work was supported by the China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (No. DY125-15-R-03); the National Natural Science Foundation of China (No. 41276173); the Zhejiang Provincial Natural Science Foundation of China (No. LQ13D060002) and the Scientific Research Fund of the Second Institute of Oceanography, SOA (No. JT1305).</p></sec><ref-list><ref id="B1"><mixed-citation publication-type="journal"><name><surname>Valls</surname><given-names>M</given-names></name><name><surname>de Lorenzo</surname><given-names>V</given-names></name><article-title>Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution</article-title><source>FEMS Microbiol Rev</source><year>2002</year><volume>26</volume><issue>4</issue><fpage>327</fpage><lpage>338</lpage><pub-id pub-id-type="doi">10.1111/j.1574-6976.2002.tb00618.x</pub-id><pub-id pub-id-type="pmid">12413663</pub-id></mixed-citation></ref><ref id="B2"><mixed-citation publication-type="journal"><name><surname>Nies</surname><given-names>DH</given-names></name><article-title>Microbial heavy-metal resistance</article-title><source>Appl Microbiol Biotechnol</source><year>1999</year><volume>51</volume><issue>6</issue><fpage>730</fpage><lpage>50</lpage><pub-id pub-id-type="doi">10.1007/s002530051457</pub-id><pub-id pub-id-type="pmid">10422221</pub-id></mixed-citation></ref><ref id="B3"><mixed-citation publication-type="journal"><name><surname>Özdemir</surname><given-names>S</given-names></name><name><surname>Kilinc</surname><given-names>E</given-names></name><name><surname>Poli</surname><given-names>A</given-names></name><name><surname>Nicolaus</surname><given-names>B</given-names></name><name><surname>Güven</surname><given-names>K</given-names></name><article-title>Cd, Cu, Ni, Mn and Zn resistance and bioaccumulation by thermophilic bacteria</article-title><source>Geobacillus toebii subsp. decanicus and Geobacillus thermoleovorans subsp. stromboliensis. 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