De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape
Identifieur interne : 000371 ( Ncbi/Merge ); précédent : 000370; suivant : 000372De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape
Auteurs : Benjamin J. Tully [États-Unis] ; Joanne B. Emerson [États-Unis] ; Karen Andrade [États-Unis] ; Jochen J. Brocks [Australie] ; Eric E. Allen [États-Unis] ; Jillian F. Banfield [États-Unis] ; Karla B. Heidelberg [États-Unis]Source :
- Archaea [ 1472-3646 ] ; 2015.
Abstract
Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon,
Url:
DOI: 10.1155/2015/875784
PubMed: 25709557
PubMed Central: 4330952
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Tully</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Emerson, Joanne B" sort="Emerson, Joanne B" uniqKey="Emerson J" first="Joanne B." last="Emerson">Joanne B. 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Tully</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Emerson, Joanne B" sort="Emerson, Joanne B" uniqKey="Emerson J" first="Joanne B." last="Emerson">Joanne B. Emerson</name><affiliation wicri:level="1"><nlm:aff id="I2">Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309</wicri:regionArea><wicri:noRegion>CO 80309</wicri:noRegion></affiliation></author><author><name sortKey="Andrade, Karen" sort="Andrade, Karen" uniqKey="Andrade K" first="Karen" last="Andrade">Karen Andrade</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720</wicri:regionArea><wicri:noRegion>CA 94720</wicri:noRegion></affiliation></author><author><name sortKey="Brocks, Jochen J" sort="Brocks, Jochen J" uniqKey="Brocks J" first="Jochen J." last="Brocks">Jochen J. Brocks</name><affiliation wicri:level="1"><nlm:aff id="I4">Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200</wicri:regionArea><wicri:noRegion>ACT 0200</wicri:noRegion></affiliation></author><author><name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E." last="Allen">Eric E. Allen</name><affiliation wicri:level="1"><nlm:aff id="I5">Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202</wicri:regionArea><wicri:noRegion>CA 92093-0202</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I6">Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093</wicri:regionArea><wicri:noRegion>CA 92093</wicri:noRegion></affiliation></author><author><name sortKey="Banfield, Jillian F" sort="Banfield, Jillian F" uniqKey="Banfield J" first="Jillian F." last="Banfield">Jillian F. Banfield</name><affiliation wicri:level="1"><nlm:aff id="I2">Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309</wicri:regionArea><wicri:noRegion>CO 80309</wicri:noRegion></affiliation></author><author><name sortKey="Heidelberg, Karla B" sort="Heidelberg, Karla B" uniqKey="Heidelberg K" first="Karla B." last="Heidelberg">Karla B. Heidelberg</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Archaea</title><idno type="ISSN">1472-3646</idno><idno type="eISSN">1472-3654</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, <italic>Haloquadratum walsbyi</italic>. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of <italic>H. walsbyi</italic> to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in <italic>H. walsbyi</italic>. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived <italic>Haloquadratum</italic> genomes and were supported by environmental <italic>de novo</italic> sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of <italic>Haloquadratum</italic>. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the <italic>de novo</italic> environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bodaker, I" uniqKey="Bodaker I">I. Bodaker</name></author><author><name sortKey="Sharon, I" uniqKey="Sharon I">I. Sharon</name></author><author><name sortKey="Suzuki, M T" uniqKey="Suzuki M">M. T. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Archaea</journal-id><journal-id journal-id-type="iso-abbrev">Archaea</journal-id><journal-id journal-id-type="publisher-id">ARCHAEA</journal-id><journal-title-group><journal-title>Archaea</journal-title></journal-title-group><issn pub-type="ppub">1472-3646</issn><issn pub-type="epub">1472-3654</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25709557</article-id><article-id pub-id-type="pmc">4330952</article-id><article-id pub-id-type="doi">10.1155/2015/875784</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title><italic>De Novo</italic> Sequences of <italic>Haloquadratum walsbyi</italic> from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tully</surname><given-names>Benjamin J.</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Emerson</surname><given-names>Joanne B.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Andrade</surname><given-names>Karen</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Brocks</surname><given-names>Jochen J.</given-names></name><xref ref-type="aff" rid="I4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Allen</surname><given-names>Eric E.</given-names></name><xref ref-type="aff" rid="I5"><sup>5</sup></xref><xref ref-type="aff" rid="I6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Banfield</surname><given-names>Jillian F.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Heidelberg</surname><given-names>Karla B.</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA</aff><aff id="I2"><sup>2</sup>Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA</aff><aff id="I3"><sup>3</sup>Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA</aff><aff id="I4"><sup>4</sup>Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia</aff><aff id="I5"><sup>5</sup>Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA</aff><aff id="I6"><sup>6</sup>Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA</aff><author-notes><corresp id="cor1">*Benjamin J. Tully: <email>btully@usc.edu</email></corresp><fn fn-type="other"><p>Academic Editor: Timothy Williams</p></fn></author-notes><pub-date pub-type="collection"><year>2015</year></pub-date><pub-date pub-type="epub"><day>1</day><month>2</month><year>2015</year></pub-date><volume>2015</volume><elocation-id>875784</elocation-id><history><date date-type="received"><day>19</day><month>6</month><year>2014</year></date><date date-type="rev-recd"><day>2</day><month>9</month><year>2014</year></date><date date-type="accepted"><day>16</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2015 Benjamin J. Tully et al.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, <italic>Haloquadratum walsbyi</italic>. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of <italic>H. walsbyi</italic> to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in <italic>H. walsbyi</italic>. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived <italic>Haloquadratum</italic> genomes and were supported by environmental <italic>de novo</italic> sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of <italic>Haloquadratum</italic>. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the <italic>de novo</italic> environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.</p></abstract></article-meta></front><floats-group><fig id="fig1" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Inset: a gene map of the region spanning 600,000–770,000 bp along the<italic> H. walsbyi</italic> J07HQW1 genome, the corresponding regions in the other<italic> H. walsbyi</italic> genomes, and the environmental contigs. Full image: an expanded view of the region denoted in the inset. Syntenic regions are marked by matching colors. Pink arrows denote the 16 CDS segment identified as unique to the<italic> H. walsbyi</italic> J07HQW1 and C23 genomes. Environmental contigs use a long form identification number whereby the first item is the sample (e.g., LT71), the second item is the filter fraction (e.g., 0.8 <italic>μ</italic>m), the third item is the phylogenetic bin (e.g., B), and the fourth item is the scaffold number (e.g., scaffold 13). The regions represented on the gene map from each genome are as follows: J07HQW1, 610,420–769,897 bp; J07HQW2, 2,470,010–2,313,700 bp; C23, 510,000–630,000 bp; DSM16790, 510,000–610,000 bp.</p></caption><graphic xlink:href="ARCHAEA2015-875784.001"></graphic></fig><fig id="fig2" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Inset: a gene map of the region spanning 1,600,000–1,660,000 bp along the<italic> H. walsbyi</italic> J07HQW1 genome, the corresponding regions in the other<italic> H. walsbyi genomes</italic>, and the environmental contigs. Full image: an expanded view of the region denoted in the inset. Syntenic regions are marked by matching colors. Environmental contigs use a long form identification number (see <xref ref-type="fig" rid="fig1">Figure 1</xref> caption). The regions represented on the gene map from each genome are as follows: J07HQW1, 1,600,465–1,660,398 bp; J07HQW2, 3,299,582–3,359,276 bp; C23, 1,240,000–1,270,000 bp and 1,530,000–1,490,000 bp; DSM16790, 1,240,690–1,270,000 bp and 1,510,000–1,470,000 bp.</p></caption><graphic xlink:href="ARCHAEA2015-875784.002"></graphic></fig><fig id="fig3" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Inset: a gene map of the region spanning 2,619,000–2,702,000 bp along the<italic> H. walsbyi</italic> J07HQW1 genome, the corresponding regions in the other<italic> H. walsbyi genomes</italic>, and the environmental contigs. Full image: an expanded view of the region denoted in the inset. Syntenic regions are marked by matching colors. Arrows highlighted in green denote individual sequences specifically identified in the paper. Environmental contigs use a long form identification number (see <xref ref-type="fig" rid="fig1">Figure 1</xref> caption). The regions represented on the gene map from each genome are as follows: J07HQW1, 2,619,269–2,703,165 bp; J07HQW2, 1,229,374–1,314,534 bp; C23, 2,110,000–2,220,000 bp; DSM16790, 2,030,000–2,125,000 bp.</p></caption><graphic xlink:href="ARCHAEA2015-875784.003"></graphic></fig><fig id="fig4" orientation="portrait" position="float"><label>Figure 4</label><caption><p>(a) A comparison of halomucin homologs, eHmu1, found on the environmental contig LT80_0.1_scaffold_0 and the corresponding fragments of eHmu2 and eHmu3, found on the contig LT80_3.0_scaffold_9. The section indicated in the black box reveals the nature of the 28 bp deletion within eHmu2 that causes the frameshift resulting in a stop codon approx. 230 bp downstream. AAID: amino acid identity. (b) A comparison of the halomucin homolog eHmu1 and the corresponding region and annotations identified in<italic> H. </italic>sp. J07HQX50. ∗ represents the location of an 81 bp gap in a GLUG motif containing CDS from<italic> H. </italic>sp. J07HQX50. NAID: nucleic acid identity.</p></caption><graphic xlink:href="ARCHAEA2015-875784.004"></graphic></fig><table-wrap id="tab1" orientation="portrait" position="float"><label>Table 1</label><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Sample </th><th align="center" rowspan="1" colspan="1">Date </th><th align="center" rowspan="1" colspan="1">Time <break></break>(24 hr)</th><th align="center" rowspan="1" colspan="1">Temperature <break></break> (°C) [<xref rid="B11" ref-type="bibr">11</xref>]</th><th align="center" rowspan="1" colspan="1">TDS (wt%)<sup>a</sup><break></break>[<xref rid="B11" ref-type="bibr">11</xref>] </th><th align="center" rowspan="1" colspan="1">pH <break></break>[<xref rid="B11" ref-type="bibr">11</xref>] </th><th align="center" rowspan="1" colspan="1">Filter size</th><th align="center" rowspan="1" colspan="1">Number of trimmed <break></break>sequences in library</th></tr></thead><tbody><tr><td align="left" rowspan="2" colspan="1">LT71 (site 1)</td><td align="center" rowspan="1" colspan="1">Jan. 7, 2010 </td><td align="center" rowspan="1" colspan="1">07:45 </td><td align="center" rowspan="1" colspan="1">20 </td><td align="center" rowspan="1" colspan="1">32 </td><td align="center" rowspan="1" colspan="1">7.2 </td><td align="center" rowspan="1" colspan="1">0.1 </td><td align="center" rowspan="1" colspan="1">12,845,524</td></tr><tr><td align="center" rowspan="1" colspan="1">Jan. 7, 2011 </td><td align="center" rowspan="1" colspan="1">07:45 </td><td align="center" rowspan="1" colspan="1">20 </td><td align="center" rowspan="1" colspan="1">32 </td><td align="center" rowspan="1" colspan="1">7.2 </td><td align="center" rowspan="1" colspan="1">0.8 </td><td align="center" rowspan="1" colspan="1">4,357,176</td></tr><tr><td align="left" rowspan="1" colspan="1">LT75 (site 1)</td><td align="center" rowspan="1" colspan="1">Jan. 7, 2010 </td><td align="center" rowspan="1" colspan="1">20:00 </td><td align="center" rowspan="1" colspan="1">32 </td><td align="center" rowspan="1" colspan="1">36 </td><td align="center" rowspan="1" colspan="1">7.3 </td><td align="center" rowspan="1" colspan="1">0.8 </td><td align="center" rowspan="1" colspan="1">13,475,176</td></tr><tr><td align="left" rowspan="2" colspan="1">LT80 (site 1)</td><td align="center" rowspan="1" colspan="1">Jan. 9, 2010 </td><td align="center" rowspan="1" colspan="1">16:50 </td><td align="center" rowspan="1" colspan="1">45 </td><td align="center" rowspan="1" colspan="1">27 </td><td align="center" rowspan="1" colspan="1">7.1 </td><td align="center" rowspan="1" colspan="1">0.1 </td><td align="center" rowspan="1" colspan="1">20,609,138</td></tr><tr><td align="center" rowspan="1" colspan="1">Jan. 9, 2011 </td><td align="center" rowspan="1" colspan="1">16:50 </td><td align="center" rowspan="1" colspan="1">45 </td><td align="center" rowspan="1" colspan="1">27 </td><td align="center" rowspan="1" colspan="1">7.1 </td><td align="center" rowspan="1" colspan="1">3.0 </td><td align="center" rowspan="1" colspan="1">9,014,584</td></tr><tr><td align="left" rowspan="1" colspan="1">LT82 (site 1)</td><td align="center" rowspan="1" colspan="1">Jan. 10, 2010 </td><td align="center" rowspan="1" colspan="1">12:50 </td><td align="center" rowspan="1" colspan="1">33 </td><td align="center" rowspan="1" colspan="1">32 </td><td align="center" rowspan="1" colspan="1">7.2 </td><td align="center" rowspan="1" colspan="1">3.0 </td><td align="center" rowspan="1" colspan="1">15,358,950</td></tr><tr><td align="left" rowspan="2" colspan="1">LT85 (site 2)</td><td align="center" rowspan="1" colspan="1">Jan. 10, 2010 </td><td align="center" rowspan="1" colspan="1">12:50 </td><td align="center" rowspan="1" colspan="1">37 </td><td align="center" rowspan="1" colspan="1">35 </td><td align="center" rowspan="1" colspan="1">7.1 </td><td align="center" rowspan="1" colspan="1">0.1 </td><td align="center" rowspan="1" colspan="1">52,520,328</td></tr><tr><td align="center" rowspan="1" colspan="1">Jan. 10, 2011 </td><td align="center" rowspan="1" colspan="1">12:50 </td><td align="center" rowspan="1" colspan="1">37 </td><td align="center" rowspan="1" colspan="1">35 </td><td align="center" rowspan="1" colspan="1">7.1 </td><td align="center" rowspan="1" colspan="1">3.0 </td><td align="center" rowspan="1" colspan="1">7,058,560</td></tr></tbody></table><table-wrap-foot><fn><p><sup>a</sup>Total dissolved solids, weight percent.</p></fn><fn><p>Data from Temp (°C), TDS, and pH were original published in Emerson et al. 2012 [<xref rid="B23" ref-type="bibr">23</xref>].</p></fn></table-wrap-foot></table-wrap><table-wrap id="tab2" orientation="portrait" position="float"><label>Table 2</label><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Assembly comparison</th><th align="center" rowspan="1" colspan="1">Mean ratio of third round to <break></break>second round assemblies</th><th align="center" rowspan="1" colspan="1">Standard <break></break>deviation</th><th align="center" rowspan="1" colspan="1">Median</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">N50</td><td align="center" rowspan="1" colspan="1">1.28</td><td align="center" rowspan="1" colspan="1">0.48</td><td align="center" rowspan="1" colspan="1">1.20</td></tr><tr><td align="left" rowspan="1" colspan="1">Maximum Contig Length</td><td align="center" rowspan="1" colspan="1">0.76</td><td align="center" rowspan="1" colspan="1">0.24</td><td align="center" rowspan="1" colspan="1">0.74</td></tr><tr><td align="left" rowspan="1" colspan="1">Mean Contig Length</td><td align="center" rowspan="1" colspan="1">1.03</td><td align="center" rowspan="1" colspan="1">0.47</td><td align="center" rowspan="1" colspan="1">0.90</td></tr><tr><td align="left" rowspan="1" colspan="1">Total Length Contained in Contigs</td><td align="center" rowspan="1" colspan="1">1.10</td><td align="center" rowspan="1" colspan="1">0.20</td><td align="center" rowspan="1" colspan="1">1.16</td></tr></tbody></table></table-wrap><table-wrap id="tab3" orientation="portrait" position="float"><label>Table 3</label><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Genome ID </th><th align="left" rowspan="1" colspan="1">Source</th><th align="center" rowspan="1" colspan="1">Maximum<break></break>coverage</th><th align="center" rowspan="1" colspan="1">Mean<break></break>coverage </th><th align="center" rowspan="1" colspan="1">% Coverage</th><th align="center" rowspan="1" colspan="1">Number of recruited<break></break>sequences<break></break>(10<sup>6</sup>)</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>J07HQW1 </td><td align="left" rowspan="1" colspan="1">Metagenome Lake Tyrrell, AUS (2007) [<xref rid="B8" ref-type="bibr">8</xref>] </td><td align="center" rowspan="1" colspan="1">2075 </td><td align="center" rowspan="1" colspan="1">275.1 </td><td align="center" rowspan="1" colspan="1">99.96 </td><td align="center" rowspan="1" colspan="1">10.58</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>J07HQW2 </td><td align="left" rowspan="1" colspan="1">Metagenome Lake Tyrrell, AUS (2007) [<xref rid="B8" ref-type="bibr">8</xref>]</td><td align="center" rowspan="1" colspan="1">6090 </td><td align="center" rowspan="1" colspan="1">222.3 </td><td align="center" rowspan="1" colspan="1">99.7 </td><td align="center" rowspan="1" colspan="1">8.78</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. </italic>sp. J07HQX50 Scaffold 1</td><td align="left" rowspan="1" colspan="1">Metagenome Lake Tyrrell, AUS (2007) [<xref rid="B8" ref-type="bibr">8</xref>] </td><td align="center" rowspan="1" colspan="1">2101 </td><td align="center" rowspan="1" colspan="1">97.6 </td><td align="center" rowspan="1" colspan="1">84.6 </td><td align="center" rowspan="1" colspan="1">1.68</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. </italic>sp. J07HQX50 Scaffold 2</td><td align="left" rowspan="1" colspan="1">Metagenome Lake Tyrrell, AUS (2007) [<xref rid="B8" ref-type="bibr">8</xref>] </td><td align="center" rowspan="1" colspan="1">2064 </td><td align="center" rowspan="1" colspan="1">98 </td><td align="center" rowspan="1" colspan="1">83.4 </td><td align="center" rowspan="1" colspan="1">1.6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>C23 </td><td align="left" rowspan="1" colspan="1">Cultured isolate from Geelong, AUS [<xref rid="B23" ref-type="bibr">23</xref>] </td><td align="center" rowspan="1" colspan="1">3387 </td><td align="center" rowspan="1" colspan="1">254.2 </td><td align="center" rowspan="1" colspan="1">92.3 </td><td align="center" rowspan="1" colspan="1">8.754</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>C23 Plasmid PL6A</td><td align="left" rowspan="1" colspan="1">Cultured isolate from Geelong, AUS [<xref rid="B23" ref-type="bibr">23</xref>] </td><td align="center" rowspan="1" colspan="1">240 </td><td align="center" rowspan="1" colspan="1">45.4 </td><td align="center" rowspan="1" colspan="1">98.2 </td><td align="center" rowspan="1" colspan="1">0.00332</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>C23 Plasmid PL6B</td><td align="left" rowspan="1" colspan="1">Cultured isolate from Geelong, AUS [<xref rid="B23" ref-type="bibr">23</xref>] </td><td align="center" rowspan="1" colspan="1">484 </td><td align="center" rowspan="1" colspan="1">90.1 </td><td align="center" rowspan="1" colspan="1">98.6 </td><td align="center" rowspan="1" colspan="1">0.006635</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>C23 Plasmid PL100</td><td align="left" rowspan="1" colspan="1">Cultured isolate from Geelong, AUS [<xref rid="B23" ref-type="bibr">23</xref>] </td><td align="center" rowspan="1" colspan="1">1016 </td><td align="center" rowspan="1" colspan="1">80.1 </td><td align="center" rowspan="1" colspan="1">95.9 </td><td align="center" rowspan="1" colspan="1">0.086</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>DSM16790 </td><td align="left" rowspan="1" colspan="1">Cultured isolate from Alicante, Spain [<xref rid="B15" ref-type="bibr">15</xref>] </td><td align="center" rowspan="1" colspan="1">3368 </td><td align="center" rowspan="1" colspan="1">254.9 </td><td align="center" rowspan="1" colspan="1">93.3 </td><td align="center" rowspan="1" colspan="1">8.76</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>H. walsbyi </italic>DSM16790 Plasmid</td><td align="left" rowspan="1" colspan="1">Cultured isolate from Alicante, Spain [<xref rid="B15" ref-type="bibr">15</xref>] </td><td align="center" rowspan="1" colspan="1">515 </td><td align="center" rowspan="1" colspan="1">66.1 </td><td align="center" rowspan="1" colspan="1">71.5 </td><td align="center" rowspan="1" colspan="1">0.034</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>Australie</li><li>États-Unis</li></country><region><li>Californie</li></region><settlement><li>Los Angeles</li></settlement><orgName><li>Université de Californie du Sud</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Tully, Benjamin J" sort="Tully, Benjamin J" uniqKey="Tully B" first="Benjamin J." last="Tully">Benjamin J. Tully</name></region><name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E." last="Allen">Eric E. Allen</name><name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E." last="Allen">Eric E. Allen</name><name sortKey="Andrade, Karen" sort="Andrade, Karen" uniqKey="Andrade K" first="Karen" last="Andrade">Karen Andrade</name><name sortKey="Banfield, Jillian F" sort="Banfield, Jillian F" uniqKey="Banfield J" first="Jillian F." last="Banfield">Jillian F. Banfield</name><name sortKey="Emerson, Joanne B" sort="Emerson, Joanne B" uniqKey="Emerson J" first="Joanne B." last="Emerson">Joanne B. Emerson</name><name sortKey="Heidelberg, Karla B" sort="Heidelberg, Karla B" uniqKey="Heidelberg K" first="Karla B." last="Heidelberg">Karla B. Heidelberg</name></country><country name="Australie"><noRegion><name sortKey="Brocks, Jochen J" sort="Brocks, Jochen J" uniqKey="Brocks J" first="Jochen J." last="Brocks">Jochen J. 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