Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

Handle URI:
http://hdl.handle.net/10754/592835
Title:
Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs
Authors:
Jimenez Infante, Francy M. ( 0000-0002-5243-1027 ) ; Ngugi, David ( 0000-0002-0442-4279 ) ; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan; Blom, Jochen; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Stingl, Ulrich ( 0000-0002-0684-2597 )
Abstract:
The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.
KAUST Department:
Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs 2015:AEM.02852-15 Applied and Environmental Microbiology
Publisher:
American Society for Microbiology
Journal:
Applied and Environmental Microbiology
Issue Date:
11-Dec-2015
DOI:
10.1128/AEM.02852-15
Type:
Article
ISSN:
0099-2240; 1098-5336
Additional Links:
http://aem.asm.org/lookup/doi/10.1128/AEM.02852-15
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.authorAlam, Intikhaben
dc.contributor.authorKamau, Allanen
dc.contributor.authorBlom, Jochenen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorStingl, Ulrichen
dc.date.accessioned2016-01-05T07:31:11Zen
dc.date.available2016-01-05T07:31:11Zen
dc.date.issued2015-12-11en
dc.identifier.citationComprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs 2015:AEM.02852-15 Applied and Environmental Microbiologyen
dc.identifier.issn0099-2240en
dc.identifier.issn1098-5336en
dc.identifier.doi10.1128/AEM.02852-15en
dc.identifier.urihttp://hdl.handle.net/10754/592835en
dc.description.abstractThe OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.urlhttp://aem.asm.org/lookup/doi/10.1128/AEM.02852-15en
dc.rightsArchived with thanks to Applied and Environmental Microbiologyen
dc.titleComprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophsen
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.journalApplied and Environmental Microbiologyen
dc.eprint.versionPost-printen
dc.contributor.institutionBioinformatics and Systems Biology, Justus Liebig University, D-35392 Giessen, Germanyen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorJimenez Infante, Francy M.en
kaust.authorNgugi, Daviden
kaust.authorVinu, Manikandanen
kaust.authorAlam, Intikhaben
kaust.authorKamau, Allanen
kaust.authorBajic, Vladimir B.en
kaust.authorStingl, Ulrichen
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