Abstract
BackgroundThe genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.ResultsThe genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.ConclusionsD. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.
Highlights
The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome
The number of horizontally transferred genes that putatively originated from organisms above the level of the Peptococcaceae family was 264 in DCB-2 and 285 in Y51
The genomic analysis of D. hafniense DCB-2 described in this paper suggests that the strain is highly self-sufficient in various aspects of metabolism and adaptation
Summary
The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome. Most of Desulfitobacterium species were isolated for their ability to reductively dehalogenate organic compounds which are, in some cases, highly resistant to Desulfitobacterium is distinguished in its use of a broad range of electron acceptors (As(V), Fe(III), U (VI), Cr (VI), Se(VI), Mn(IV), S°, S O. Nine strains have been identified to date that belong to D. hafniense species including D. hafniense Y51 which was isolated from a Japanese soil contaminated with tetrachloroethene [8], and for which the complete genome sequence was reported [1,9]. We report here on the genome sequence of D. hafniense DCB-2 with specific reference to its metal reduction and dehalogenation abilities, in addition to the comparison with strain Y51. We provide results from expression arrays that complement the genomic data
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