title: Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.
abstract: The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play 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 (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster 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 the H-RS cluster 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 complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Francy
authors.initials: F
authors.lastname: Jimenez-Infante
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: David Kamanda
authors.initials: DK
authors.lastname: Ngugi
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Manikandan
authors.initials: M
authors.lastname: Vinu
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Intikhab
authors.initials: I
authors.lastname: Alam
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Allan Anthony
authors.initials: AA
authors.lastname: Kamau
authors.affiliation: Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia uli.stingl@kaust.edu.sa.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Stingl
mesh_terms: D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D060146:Ecotype; D023281:Genomics; D019156:Indian Ocean; D042762:Methylophilaceae / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer