期刊
STANDARDS IN GENOMIC SCIENCES
卷 13, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s40793-017-0306-7
关键词
Pseudomonas alcaliphila JAB1; Pseudomonadaceae; Genome; Dioxygenase; Monooxygenase; Biodegradation; Bioremediation; Aromatic compounds; Biphenyl; Polychlorinated biphenyls (PCBs); Chlorobenzoic acids (CBAs); cis-1,2-dichloroethylene (cDCE); Phenol; bph genes; ben genes; phe genes; MALDI-TOF MS
资金
- Czech Science Foundation [13-28283S, 14-32432S]
In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the beta-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level.
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