Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic.
Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 40 Prague, Czech Republic.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkaa030.
Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.
某些工业化学品由于其顽固的特性而在环境中积累。生物修复利用某些环境细菌分解这些化学物质并减轻污染的能力。一种这样的细菌菌株，命名为 Pvy，是从罗马尼亚一个位于炼油厂附近的泻湖的沉积物样本中分离出来的，因为它能够降解二苯并呋喃（DF）。使用 Oxford Nanopore MiniION 平台获得了 Pvy 菌株的基因组序列。根据从基因组中包含的六个 16S rRNA 基因拷贝和同源平均核苷酸同一性（OrthoANI）计算编译的共识 16S rRNA 基因序列，Pvy 菌株被鉴定为假单胞菌 veronii，这证实了借助 MALDI-TOF 质谱和 MALDI BioTyper 获得的鉴定。对负责菌株整体生物降解多功能性的酶进行了基因组分析。Pvy 菌株能够从萘（NP）和几种天然来源的芳香族化合物中获取碳，包括水杨酸、原儿茶酸、对羟基苯甲酸、反式肉桂酸、香草酸和吲哚乙酸或香草醛，并且被证明能够降解但不能利用 DF。在 Pvy 基因组中总共发现了七个基因座，这使该菌株能够参与这些芳香族化合物的降解。我们的实验数据还表明，携带 Pvy 菌株质粒的 NP-双加氧酶 α 亚基基因（ndoB）的转录可被 DF 诱导。这些特征使 Pvy 菌株成为各种生物修复应用的潜在候选者。
