Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point

Handle URI:
http://hdl.handle.net/10754/627690
Title:
Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point
Authors:
Zhang, Weipeng; Tian, Ren-Mao; Sun, Jin; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Ding, Wei; Cai, Lin; Lan, Yi; Tong, Haoya; Li, Yongxin; Jamieson, Alan J.; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Drazen, Jeffrey C.; Bartlett, Douglas; Qian, Pei-Yuan
Abstract:
Amphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth's oceans. Here the gut microbiota of the amphipod Hirondellea gigas collected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated by Psychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-living Psychromonas strains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamine N-oxide (TMAO) reducing gene cluster in CDP1, suggesting that the
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC)
Citation:
Zhang W, Tian R-M, Sun J, Bougouffa S, Ding W, et al. (2018) Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point. mSystems 3: e00009–18. Available: http://dx.doi.org/10.1128/msystems.00009-18.
Publisher:
American Society for Microbiology
Journal:
mSystems
Issue Date:
25-Apr-2018
DOI:
10.1128/msystems.00009-18
PubMed ID:
29657971
Type:
Article
ISSN:
2379-5077
Sponsors:
The investigations and samplings for this study were done with the permission of U.S. Fish and Wildlife Service (the Micronesia permit number is FM14-KY01401RS-01, and the USFW permit number is 2014-003). We thank the crew of the RV Falkor on the Schmidt Ocean Institute-funded cruises to Challenger Deep and Sirena Deep. We thank John B. Hanks and Craig Kapfer for their support while performing some of the computational work on Dragon and Snapdragon compute clusters of the Computational Bioscience Research Center at the King Abdullah University of Science and Technology. This study was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB06010102) and the Nature Science Foundation of China (U1301232).
Additional Links:
http://msystems.asm.org/content/3/3/e00009-18
Appears in Collections:
Articles; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorZhang, Weipengen
dc.contributor.authorTian, Ren-Maoen
dc.contributor.authorSun, Jinen
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorDing, Weien
dc.contributor.authorCai, Linen
dc.contributor.authorLan, Yien
dc.contributor.authorTong, Haoyaen
dc.contributor.authorLi, Yongxinen
dc.contributor.authorJamieson, Alan J.en
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorDrazen, Jeffrey C.en
dc.contributor.authorBartlett, Douglasen
dc.contributor.authorQian, Pei-Yuanen
dc.date.accessioned2018-04-30T06:58:23Z-
dc.date.available2018-04-30T06:58:23Z-
dc.date.issued2018-04-25en
dc.identifier.citationZhang W, Tian R-M, Sun J, Bougouffa S, Ding W, et al. (2018) Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point. mSystems 3: e00009–18. Available: http://dx.doi.org/10.1128/msystems.00009-18.en
dc.identifier.issn2379-5077en
dc.identifier.pmid29657971-
dc.identifier.doi10.1128/msystems.00009-18en
dc.identifier.urihttp://hdl.handle.net/10754/627690-
dc.description.abstractAmphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth's oceans. Here the gut microbiota of the amphipod Hirondellea gigas collected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated by Psychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-living Psychromonas strains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamine N-oxide (TMAO) reducing gene cluster in CDP1, suggesting that theen
dc.description.sponsorshipThe investigations and samplings for this study were done with the permission of U.S. Fish and Wildlife Service (the Micronesia permit number is FM14-KY01401RS-01, and the USFW permit number is 2014-003). We thank the crew of the RV Falkor on the Schmidt Ocean Institute-funded cruises to Challenger Deep and Sirena Deep. We thank John B. Hanks and Craig Kapfer for their support while performing some of the computational work on Dragon and Snapdragon compute clusters of the Computational Bioscience Research Center at the King Abdullah University of Science and Technology. This study was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB06010102) and the Nature Science Foundation of China (U1301232).en
dc.publisherAmerican Society for Microbiologyen
dc.relation.urlhttp://msystems.asm.org/content/3/3/e00009-18en
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectAmphipoden
dc.subjectGut Microbiotaen
dc.subjectMariana Trenchen
dc.subjectPsychromonasen
dc.titleGenome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Pointen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalmSystemsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDivision of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.en
dc.contributor.institutionSchool of Marine Science and Technology, Newcastle University, Newcastle Upon Tyne, Tyne and Wear, United Kingdom.en
dc.contributor.institutionDepartment of Oceanography, University of Hawaii at Manoa, Honolulu, Hawaii, USA.en
dc.contributor.institutionMarine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.en
kaust.authorBougouffa, Salimen
kaust.authorBajic, Vladimir B.en

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.