Draft Genome Sequence of Methylophaga aminisulfidivorans MP
            <sup>T</sup>

Methylophaga sp. strains JAM1 and JAM7 have been isolated from a denitrification system. Strain JAM1 was the first Methylophaga strain reported to be able to grow under denitrifying conditions. Here, we report the complete genome sequences of the two strains, which allowed prediction of gene clusters involved in denitrification in strain JAM1. Members of the genus Methylophaga (gammaproteobacteria) are methane-utilizing methylotrophs, typically isolated from marine environments or brackish waters (1, 5-8, 11, 12). Genome sequences have been reported for M. thiooxydans (strain DMS010T) (4) and M. aminisulfidivorans (strain MP T ) (10). Methylophaga sp. strains JAM1 and JAM7 have been isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome (2). Strain JAM1 has the particularity among Methylophaga species to grow under denitrifying conditions in the presence of nitrate and methanol.The genome sequences of strain JAM1 (586,834 reads, 35ϫ coverage) and strain JAM7 (546,596 reads, 35ϫ coverage) consist of one chromosome (3,137,192 bp) for strain JAM1 and one chromosome (2,697,465 bp) and one plasmid (47,825 bp, 63ϫ coverage) for strain JAM7. The sequences were determined using the Roche Genome Sequencer FLX system and titanium chemistry (paired ends with an insert size of 2.7 kb). Primary assembly of the sequencing reads was carried out with Newbler gsAssembler version 2.5.3 (Roche) to generate scaffolds from a 454 paired-end library. After multiple rounds of gap-closing steps using CONSED version 20.0 (9) and synteny with M. aminosulfidivorans (AFIG00000000), a single contig representing the chromosome was obtained for each strain. The genome sequencing and assembly were performed at the Plateforme d'Analyses Génomiques from the Institut de Biologie Intégrative et des Systèmes (IBISUniversité Laval, Québec, Canada). The genome sequences were uploaded into Integrated Microbial Genomes Expert Review (IMG/ER) (https://img.jgi.doe.gov/cgi-bin/er/main.cgi) to be annotated.The chromosome of strain JAM1 harbors 3,043 predicted coding open reading frames (ORFs), of which 2,476 have a predicted function. There are 3 rRNA operons (5S, 16S, 23S) and 44 tRNAs corresponding to 20 structural amino acids. The chromosome of strain JAM7 harbors 2,698 ORFs, of which 2,194 have a predicted function, 3 rRNA operons, and 41 tRNAs corresponding to 20 structural amino acids, whereas 56 ORFs were found in the plasmid. For both strains, the mxaDEFJGIRACKL gene cluster, encoding the methanol dehydrogenase, was predicted. Both genomes predict to encode all the genes of the Emden-Meyerhof-Parnas (glycolysis) pathway and of the Entner-Doudoroff variant of the ribulose monophosphate (RuMP) pathway. The latter pathway is the one used by the other Methylophaga species to assimilate one-carbon substrate (3).Growth of strain JAM1 under denitrifying conditions by reducing nitrate into nitrite was shown to be correlated with the presence of two nitrate reductase narG genes (2). The strain JAM1 genome sequence confi...

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“…Genome sequences have been reported for M. thiooxydans (strain DMS010T) (4) and M. aminisulfidivorans (strain MP T ) (10). Methylophaga sp.…”

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confidence: 99%

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7

et al. 2012

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“…Rv2025c is de-repressed by Ni 2+ and Co 2+ , is controlled by the high-affinity Ni 2+ /Co 2+ sensor KmtR and may use Ni 2+ as a substrate ( Cubillas et al , 2013 ). Candidate ‘denovo003460' has homology to an inferred ABC-type dipeptide/oligopeptide/nickel transport system in Methylophaga aminisulfidivorans ( Han et al , 2011 ). Accessory gene candidate ‘GI:13475426' is annotated as a nickel–cobalt–cadmium resistance protein in Mesorhizobium huakuii bv.…”

Section: Discussionmentioning

confidence: 99%

“…Genes in the ncc operon share close homology with those in the cnr operon, a cobalt nickel efflux system integral to nickel tolerance in Bradyrhizobium from serpentine soil ( Chaintreuil et al , 2007 ). Candidate ‘denovo003135'is homologous to a putative nickel import ATP-binding protein, NikD, in Methlyophaga thiooxydans DMS010 ( Han et al , 2011 ).…”

Section: Discussionmentioning

confidence: 99%

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium

et al. 2016

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The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil. Our study uses whole-genome sequencing to describe the pan-genome of a focal clade of wild mesorhizobia that show contrasting levels of nickel adaptation despite high relatedness (99.8% identity at 16S). We observe ecotypic specialization within an otherwise genomically cohesive population, rather than finding distinct specialized bacterial lineages in contrasting soil types. This finding supports recent reports that heterogeneous environments impose selection that maintains differentiation only at a small fraction of the genome. Our work further uses a genome-wide association study to propose candidate genes for nickel adaptation. Several candidates show homology to genetic systems involved in nickel tolerance and one cluster of candidates correlates perfectly with soil origin, which validates our approach of ascribing genomic variation to adaptive divergence.

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“…buryatica'; Doronina et al, 2003b), although these names have not been validly published and the strains are therefore not included in the updated description. Genome sequences are now available for M. aminisulfidivorans (Han et al, 2011) and M. thiooxydans , and will assist in further characterization of members of this genus.…”

mentioning

confidence: 99%

“…A number of other strains have been designated species of the genus Methylophaga , namely ‘ M. limanica ’ (Doronina et al , 1997) and ‘ M. natronica ’ (also known as ‘ M. buryatica ’; Doronina et al , 2003b), although these names have not been validly published and the strains are therefore not included in the updated description. Genome sequences are now available for M. aminisulfidivorans (Han et al , 2011) and M. thiooxydans (Boden et al , 2011), and will assist in further characterization of members of this genus.…”

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Emended description of the genus Methylophaga Janvier et al. 1985

Boden

2012

International Journal of Systematic and Evolutionary Microbiology

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The genus Methylophaga Janvier et al. 1985 comprises eight species with validly published names at the time of writing. The original description of the genus was published over 26 years ago and was based on only two species, namely Methylophaga marina and Methylophaga thalassica -as such, the description of the genus requires updating to take into account the other six known species. Based on literature concerning the eight species of Methylophaga published over the last 26 years, an emended description of the genus is presented, taking into account properties of all members of the species with validly published names.The genus Methylophaga was designated in 1985 following the isolation of a novel species of halophilic marine methylotrophic gammaproteobacteria, named Methylophaga marina, and the reclassification of 'Methylomonas thalassica' as Methylophaga thalassica (Janvier et al., 1985). The description of the genus was based on a number of strains of the only two species then known, and indicates that all members of the genus are 'auxotrophic for B 12 ' and 'isolated from marine environments'. The phylogenetic positions, with respect to 16S rRNA gene sequences, of the eight Methylophaga species with validly published names are shown in Fig. 1. It can be seen that the three alkaliphilic species, M. alcalica, M. lonarensis and M. muralis, form a distinct clade away from that containing the type species (M. marina) -this is consistent with the relatively low identities of these sequences to that of the type species, as shown in Table 1. Additionally, the DNA G+C contents of M. alcalica and M. lonarensis are the highest within the genus (see Table 1), although that of M. muralis is more similar to those of non-alkaliphilic species. Further studies into the chemotaxonomic properties of the three alkaliphilic Methylophaga species, along with DNA-DNA hybridization against M. marina, are required to verify their position, although, for the sake of this emendation, they are included in the genus Methylophaga.Differential physiological and chemotaxonomic properties are given in Table 2. It can be seen that the predominant cellular fatty acids have only been determined in half of the species, although palmitic (C 16 : 0 ) and palmitoleic (C 16 : 1 ) acids are found in all species analysed and vaccenic acid (C 18 : 1v7c ) predominates in all of the alkaliphilic species; it is also present at low levels (2.3 %) in M. aminisulfidivorans (Kim et al., 2007). Dominant cellular phospholipids are phosphatidylethanolamine and phosphatidylglycerol in those species analysed (M. alcalica, M. aminisulfidivorans, M. lonarensis and M. muralis; references in Table 2). Given that these parameters have not been determined for the type species, they are not included in the emended description, but are included here for completeness. In terms of substrate ranges, M. lonarensis appears to be the most restricted, growing only on methanol, which is a substrate common to all members of the genus, although the majority also grow on monomethyl...

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Draft Genome Sequence of Methylophaga aminisulfidivorans MP ^T

Cited by 12 publications

References 7 publications

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium

Emended description of the genus Methylophaga Janvier et al. 1985

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Draft Genome Sequence of Methylophaga aminisulfidivorans MP T

Cited by 12 publications

References 7 publications

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium

Emended description of the genus Methylophaga Janvier et al. 1985

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Draft Genome Sequence of Methylophaga aminisulfidivorans MP ^T