Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5

Abstract

Background: Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium capable of utilizing CO (carbon monoxide) and fixing CO2 (carbon dioxide). We previously published the draft genome of this organism and recently submitted the complete genome sequence to GenBank.

Results: The genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5 consists of a 3.74-Mb chromosome and a 133-kb megaplasmid that contains the genes responsible for utilization of carbon monoxide, carbon dioxide, and hydrogen. To our knowledge, this strain is the first one to be sequenced in the genus Oligotropha, the closest fully sequenced relatives being Bradyrhizobium sp. BTAi and USDA110 and Nitrobacter hamburgiensis X14. Analysis of the O. carboxidovorans genome reveals potential links between plasmid-encoded chemolithoautotrophy and chromosomally-encoded lipid metabolism. Comparative analysis of O. carboxidovorans with closely related species revealed differences in metabolic pathways, particularly in carbohydrate and lipid metabolism, as well as transport pathways.

Conclusion: Oligotropha, Bradyrhizobium sp and Nitrobacter hamburgiensis X14 are phylogenetically proximal. Although there is significant conservation of genome organization between the species, there are major differences in many metabolic pathways that reflect the adaptive strategies unique to each species.

Figure 1

Circular representation of the O. carboxidovorans OM5 genome. Circles display (from inside): genomic position in kilobases, GC-skew, GC content, BLASTX results with strain B. japonicum strain USDA110 (blast 2), BLASTX results with N. hamburgensis strain X14 (blast 1), predicted protein-coding sequences (CDS) on the reverse strand, and predicted CDS on the forward strand. Protein-coding sequences on the outer two circles are colored according to predicted COG (clusters of orthologous groups) functional categories. The single letter COG group identifications are described in Table 2.

Figure 2

Phylogenetic tree on the basis of 16 S rRNA genes for O. carboxidovorans OM5, B. japonicum USDA110, Nitrobacter hamburgensis X14, and Bradyrhizobium sp. BTAi1 where Arthrobacter was used as outgroup. The tree was created using Treecon. Bootstrapping is shown for values 70% and above. The tree is based on distance matrix where 0.1 means 10% difference between two sequences.