文章基本信息

标题：Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants
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作者：Jakub Ridl ; Jachym Suman ; Serena Fraraccio 等
期刊名称：Environmental Microbiome
印刷版ISSN：2524-6372
出版年度：2018
卷号：13
期号：1
页码：1-10
DOI：10.1186/s40793-017-0306-7
摘要：In this study, following its isolation from contaminated soil, the genomic sequence of strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The 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, 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 β-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.
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