Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats

Handle URI:
http://hdl.handle.net/10754/563555
Title:
Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats
Authors:
Jimenez Infante, Francy M. ( 0000-0002-5243-1027 ) ; Ngugi, David ( 0000-0002-0442-4279 ) ; Alam, Intikhab; Rashid, Mamoon ( 0000-0003-4851-4994 ) ; Ba Alawi, Wail ( 0000-0002-2747-4703 ) ; Kamau, Allan; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Stingl, Ulrich ( 0000-0002-0684-2597 )
Abstract:
Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group. © 2014 Federation of European Microbiological Societies.
KAUST Department:
Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program; Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Marine Microbial Ecology Research Group
Publisher:
Oxford University Press (OUP)
Journal:
FEMS Microbiology Ecology
Issue Date:
22-May-2014
DOI:
10.1111/1574-6941.12348
PubMed ID:
24785133
Type:
Article
ISSN:
01686496
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Marine Science Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; 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.authorAlam, Intikhaben
dc.contributor.authorRashid, Mamoonen
dc.contributor.authorBa Alawi, Wailen
dc.contributor.authorKamau, Allanen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorStingl, Ulrichen
dc.date.accessioned2015-08-03T11:54:22Zen
dc.date.available2015-08-03T11:54:22Zen
dc.date.issued2014-05-22en
dc.identifier.issn01686496en
dc.identifier.pmid24785133en
dc.identifier.doi10.1111/1574-6941.12348en
dc.identifier.urihttp://hdl.handle.net/10754/563555en
dc.description.abstractUsing dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group. © 2014 Federation of European Microbiological Societies.en
dc.publisherOxford University Press (OUP)en
dc.subjectAlphaproteobacteriaen
dc.subjectDilution-to-extinctionen
dc.subjectOCS116 cladeen
dc.subjectProteorhodopsinen
dc.subjectPS1 cladeen
dc.subjectRed Seaen
dc.titleGenomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitatsen
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.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentMarine Science Programen
dc.contributor.departmentMarine Microbial Ecology Research Groupen
dc.identifier.journalFEMS Microbiology Ecologyen
kaust.authorNgugi, Daviden
kaust.authorAlam, Intikhaben
kaust.authorRashid, Mamoonen
kaust.authorBajic, Vladimir B.en
kaust.authorStingl, Ulrichen
kaust.authorJimenez Infante, Francy M.en
kaust.authorBa Alawi, Wailen
kaust.authorKamau, Allanen

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