De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape
Identifieur interne : 000115 ( Main/Exploration ); précédent : 000114; suivant : 000116De 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
Affiliations:
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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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Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S. F. Altschul</name></author><author><name sortKey="Madden, T L" uniqKey="Madden T">T. L. Madden</name></author><author><name sortKey="Sch Ffer, A A" uniqKey="Sch Ffer A">A. A. Schäffer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nishihara, M" uniqKey="Nishihara M">M. Nishihara</name></author><author><name sortKey="Yamazaki, T" uniqKey="Yamazaki T">T. Yamazaki</name></author><author><name sortKey="Oshima, T" uniqKey="Oshima T">T. Oshima</name></author><author><name sortKey="Koga, Y" uniqKey="Koga Y">Y. Koga</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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. Brocks</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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