The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments

Members of the gram-negative, strictly aerobic genus Comamonas occur in various environments. Here we report the complete genome of Comamonas testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2 genome has many genes for transportation (22%) and signal transduction (6%), which allows the cells to respond and adapt to changing environments. Strain CNB-2 does not assimilate carbohydrates due to the lack of genes encoding proteins involved in glycolysis and pentose phosphate pathways, and it contains many genes encoding proteins involved in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to take up and metabolize a range of carboxylic acids. This nutritional bias for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy unique niches in environments. Four different sets of terminal oxidases for the respiratory system were identified, and they putatively functioned at different oxygen concentrations. This study conclusively revealed at the genomic level that the genetic versatility of C. testosteroni is vital for competition with other bacteria in its special niches.The members of the genus Comamonas are gram-negative, strict aerobes and frequently occur in diverse habitats, including activated sludge, marshes, marine habitats, and plant and animal tissues (4, 12, 13). They grow on organic acids, amino acids, and peptone, but they rarely attack carbohydrates. Some species, such as Comamonas testosteroni, can also mineralize complex and xenobiotic compounds, such as testosterone (17) and 4-chloronitrobenzene (CNB) (54). Their diversified niches make Comamonas species environmentally important and also suggest that the genus Comamonas represents a group of bacteria that can adapt very well, both ecologically and physiologically, to environments.To understand better how environmental microbes adapt to their environments, many well-known environmental microbes, such as Pseudomonas putida (53) and Rhodococcus sp. strain RAH1 (31), have been sequenced. The genome data for these organisms, as well as other environmental microbes, provide not only an understanding of physiological and environmental functions at the genetic level but also a starting point for systems biology analyses of these microbes. Until now, none of the Comamonas species has been sequenced, although these organisms represent an important group of environmental microbes.C. testosteroni strain CNB-1 was isolated from CNB-contaminated activated sludge and grows with CNB as a sole source of carbon and nitrogen, and it has been used successfully for rhizoremediation of CNB-polluted soil (25). Strain CNB-1 has a circular chromosome and a large plasmid, and the genes involved in the degradation of CNB on plasmid pCNB1 were identified previously (28). In the present study, the genome of strain CNB-2, which was derived from strain CNB-1, was sequenced, and a genome analysis was performed parallel to physiological experiments. The aim of this work was to obtain genetic insight into how C. testosteroni adapts to changing and diverse environments.