The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA-DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.

• Klíčová slova
• PAH, PCB, Rhodococcus, biodegradation, complete genome, hydrocarbons,
• MeSH
• alkylační opravný homolog genetika   metabolismus   MeSH
• biodegradace MeSH
• fylogeneze MeSH
• naftaleny metabolismus   MeSH
• polychlorované bifenyly chemie   MeSH
• Rhodococcus klasifikace   genetika   růst a vývoj   MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenování celého genomu metody   MeSH
• shluková analýza MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• xyleny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• alkylační opravný homolog MeSH
• naftaleny MeSH
• naphthalene MeSH Prohlížeč
• polychlorované bifenyly MeSH
• RNA ribozomální 16S MeSH
• xyleny MeSH

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.

• MeSH
• Bacteria klasifikace   genetika   izolace a purifikace   metabolismus   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• benzen metabolismus   MeSH
• benzenové deriváty metabolismus   MeSH
• biodegradace MeSH
• biodiverzita MeSH
• látky znečišťující půdu metabolismus   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• toluen metabolismus   MeSH
• xyleny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Brazílie MeSH
• Česká republika MeSH
• Švýcarsko MeSH
• Názvy látek
• bakteriální proteiny MeSH
• benzen MeSH
• benzenové deriváty MeSH
• ethylbenzene MeSH Prohlížeč
• látky znečišťující půdu MeSH
• půda MeSH
• toluen MeSH
• xyleny MeSH

Several aerobic metabolic pathways for the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), which are provided by two enzymic systems (dioxygenases and monooxygenases), have been identified. The monooxygenase attacks methyl or ethyl substituents of the aromatic ring, which are subsequently transformed by several oxidations to corresponding substituted pyrocatechols or phenylglyoxal, respectively. Alternatively, one oxygen atom may be first incorporated into aromatic ring while the second atom of the oxygen molecule is used for oxidation of either aromatic ring or a methyl group to corresponding pyrocatechols or protocatechuic acid, respectively. The dioxygenase attacks aromatic ring with the formation of 2-hydroxy-substituted compounds. Intermediates of the "upper" pathway are then mineralized by either ortho- or meta-ring cleavage ("lower" pathway). BTEX are relatively water-soluble and therefore they are often mineralized by indigenous microflora. Therefore, natural attenuation may be considered as a suitable way for the clean-up of BTEX contaminants from gasoline-contaminated soil and groundwater.

• MeSH
• aerobní bakterie enzymologie   metabolismus   MeSH
• benzen metabolismus   MeSH
• benzenové deriváty metabolismus   MeSH
• biodegradace MeSH
• toluen metabolismus   MeSH
• uhlovodíky chemie   metabolismus   MeSH
• xyleny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• benzen MeSH
• benzenové deriváty MeSH
• ethylbenzene MeSH Prohlížeč
• toluen MeSH
• uhlovodíky MeSH
• xyleny MeSH