GENOME AND PHENOTYPE MICROARRAY ANALYSES OF TWO RHODOCOCCUS STRAINS WITH ENVIRONMENTAL AND INDUSTRIAL RELEVANCE

The Rhodococcus genus comprises of Gram-positive, non-motile, nonsporulating, aerobic bacteria, with a high G+C content and a mycolic acid-containing cell wall. Members of Rhodoccocus genus are widely distributed in soil, water and marine sediments; moreover, some of them are pathogens for humans and animals (R. equi) while others cause diseases of plants (R. fascians). Due to their metabolic flexibility and their tolerance to various stresses, they play an important role in nutrient cycling and have potential applications in bioremediation, biotransformations, and biocatalysis. Consistent with the wide catabolic diversity, they possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. Compared to the increasing number of Rhodococcus spp. genomes that have been sequenced, very limited studies are available on their wide metabolic abilities and on their potentials for biodegradation activities related to genomic features. The present work focuses on the analysis of metabolic capabilities and genomic features of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 that were isolated from an aerobic butane-utilizing consortium and from an aromatic hydrocarbon contaminated soil, respectively. Phylogenetic analyses and genomic comparison with correlated species were performed to characterize the unique regions present in the genome of R7 and BCP1 strains. Phenotype Microarray analysis was also conducted using the Biolog redox technology with commercially available Biolog microtiter plates (pre-loaded substrates) and with microtiter plates that were manually prepared with additional organic/ xenobiotic compounds to be tested. Compared to BCP1, R7 strain generally showed higher metabolic activities compared on the tested carbon sources and broader range of nitrogen and sulfur sources. BCP1 specifically utilized some carboxylic acids and amino fatty acids as carbon and nitrogen sources, respectively. The two strains were able to resist to various chemicals, pH values and osmolytic substances. Phenotype microarray results also highlighted new biodegradation capacities of BCP1 and R7 strains towards aliphatic and aromatic hydrocarbons as well as emergent contaminants like naphthenic acids. These metabolic data were combined with the genomic study to genetically interpret the metabolic features of these bacterial strains with potential application for bioremediation and industrial processes.