Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade

Handle URI:
http://hdl.handle.net/10754/625630
Title:
Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade
Authors:
Jimenez Infante, Francy M. ( 0000-0002-5243-1027 ) ; Ngugi, David ( 0000-0002-0442-4279 ) ; Vinu, Manikandan; Blom, Jochen ( 0000-0001-6455-3622 ) ; Alam, Intikhab; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Stingl, Ulrich ( 0000-0002-0684-2597 )
Abstract:
The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain-specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.
KAUST Department:
Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Jimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, et al. (2017) Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade. FEMS Microbiology Ecology 93. Available: http://dx.doi.org/10.1093/femsec/fix083.
Publisher:
Oxford University Press (OUP)
Journal:
FEMS Microbiology Ecology
Issue Date:
22-Jun-2017
DOI:
10.1093/femsec/fix083
Type:
Article
ISSN:
1574-6941
Sponsors:
Funding for this research was provided through baseline funds from KAUST to US.
Additional Links:
https://academic.oup.com/femsec/article-abstract/doi/10.1093/femsec/fix083/3883768/Genomic-Characterization-of-Two-Novel-SAR11
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorJimenez Infante, Francy M.en
dc.contributor.authorNgugi, Daviden
dc.contributor.authorVinu, Manikandanen
dc.contributor.authorBlom, Jochenen
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorStingl, Ulrichen
dc.date.accessioned2017-10-03T12:49:30Z-
dc.date.available2017-10-03T12:49:30Z-
dc.date.issued2017-06-22en
dc.identifier.citationJimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, et al. (2017) Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade. FEMS Microbiology Ecology 93. Available: http://dx.doi.org/10.1093/femsec/fix083.en
dc.identifier.issn1574-6941en
dc.identifier.doi10.1093/femsec/fix083en
dc.identifier.urihttp://hdl.handle.net/10754/625630-
dc.description.abstractThe SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain-specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.en
dc.description.sponsorshipFunding for this research was provided through baseline funds from KAUST to US.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/femsec/article-abstract/doi/10.1093/femsec/fix083/3883768/Genomic-Characterization-of-Two-Novel-SAR11en
dc.subjectDilution-to-extinction cultivationen
dc.subjectmarine bacteriaen
dc.subjectPelagibacteralesen
dc.subjectRed Seaen
dc.subjectSAR11en
dc.subjectSAR 11 ecotypesen
dc.titleGenomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib cladeen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalFEMS Microbiology Ecologyen
dc.contributor.institutionBioinformatics and Systems Biology, Justus Liebig University, Giessen, Germanyen
dc.contributor.institutionUniversity of Florida, UF/IFAS, Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, Davie, FL 33314, USAen
kaust.authorJimenez Infante, Francy M.en
kaust.authorNgugi, Daviden
kaust.authorVinu, Manikandanen
kaust.authorAlam, Intikhaben
kaust.authorBajic, Vladimir B.en
kaust.authorStingl, Ulrichen
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