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Orro A, Cappelletti M, D'Ursi P, Milanesi L, Di Canito A, Zampolli J, Collina E, Decorosi F, Viti C, Fedi S, Presentato A, Zannoni D, Di Gennaro P. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance. PLoS One 2015; 10:e0139467. [PMID: 26426997 PMCID: PMC4591350 DOI: 10.1371/journal.pone.0139467] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.
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Affiliation(s)
- Alessandro Orro
- Institute of Biomedical Technology, CNR, Segrate, Milano, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Alessandra Di Canito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy; Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Elena Collina
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Francesca Decorosi
- Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy
| | - Carlo Viti
- Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
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