Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Abstract

BackgroundMethylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.Methodology/Principal FindingsThe 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid).Conclusion/SignificanceThese two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.

Treatment of groundwater containing Mn(II), Fe(II), As(III) and Sb(III) by bioaugmented quartz-sand filters

“…Results also suggest that other Mnoxidizing Pseudomonas may exist in the columns as the cumA gene is frequently found in different Pseudomonas strains (Brouwers et al, 1999;de Vrind-de Jong et al, 2000). The mox genes in columns were similar to those found in genera Aurantimonas and Methylobacterium (Dick et al, 2008;Vuilleumier et al, 2009). …”

Synchronous Waves of Failed Soft Sweeps in the Laboratory: Remarkably Rampant Clonal Interference of Alleles at a Single Locus

“…Six alleles were discovered that involved transposition of an insertion sequence (IS) element (ISMex25) from a small, single-copy, endogenous plasmid (pMETA2) (Vuilleumier et al 2009) into the replication initiation gene for this plasmid, trfA (Marx and Lidstrom 2001). This event resulted in a single co-integrate consisting of the two plasmids concatenated together (Chou and Marx 2012) ( Figure 1A).…”

Phylogenetic Study of Methanol Oxidizers from Chilika-Lake Sediments Using Genomic and Metagenomic Approaches

“…For PCR amplification, final genomic DNA concentration was adjusted to 50 ng/ll. 16S rRNA gene was partially amplified using primers pA (5 0 -AGAGTTTGATCCTGGCTCAG3 0 ; E. coli position [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] and pH (5 0 -AAGGAGGTGATCCAGCCGCA3 0 ; E. coli position 1525-1544) [31]. Amplification was carried out on a thermal cycler (Biorad PTC0220) in 100 ll volume by mixing 50-90 ng template DNA with polymerase reaction buffer (109); 100 lM (each) dATP, dCTP, dTTP and dGTP; primers pA and pH (20 ng each) and 1.0 U Taq polymerase using following conditions: initial denaturation at 94°C for 1.5 min; 35 cycles at 95°C for 1.0 min, 55°C for 1.0 min, 72°C for 1.0 min; and final extension at 72°C for 5 min.…”

“…PCR-based methods facilitate the methanotrophs ecology and diversity studies, viz., 16S ribosomal RNA technology and specific amplification of 'functional genes', such as those encoding unique enzymes in the organismal metabolism including methane monooxygenase and methanol dehydrogenase. Methanol-oxidizing bacteria play significant role in biogeochemical carbon cycling by facilitating incorporation of C 1 derivatives into biomass [13,14] using methanol as the sole carbon and energy source. Cyto-and bio-chemical properties, such as, synthesis of osmoprotectants, accumulation of potassium ions, formation of glycoprotein S-layers on the outer cell wall surface, and modification of the chemical composition of their membranes, allow these specialized group (haloalkaliphilic methanotrophs) to adapt to saline and alkaline habitats [4,15].…”