The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.接种特定降解菌（生物强化，bioaugmentation）可加速苯、甲苯、乙苯、间二甲苯与对二甲苯（BTEX）污染土壤的自然修复过程。生物强化主要指引入具备代谢特性与适应潜力的细菌，使其通过降解污染物在污染环境中存活并增殖。为更好地理解细胞向污染基质转移过程中的适应性响应，本研究分析了可降解BTEX的维罗纳假单胞菌（Pseudomonas veronii）1YdBTEX2在非灭菌土壤与液体培养基中，分别在有、无甲苯条件下的基因组特征，以及全基因组范围内的短期（1小时）基因表达变化。本研究获得了维罗纳假单胞菌1YdBTEX2的无间隙基因组序列，该基因组包含3个独立复制子，总长度为8 Mb，其中2个复制子与目前已知的细菌复制子关联性极低。在土壤与液体培养基中，经1小时甲苯暴露后，多个基因簇均出现显著转录上调（最大诱导倍数达208倍），涵盖甲苯降解通路、趋化系统以及甲苯外排泵相关基因簇。这充分印证了这些基因簇在甲苯适应性响应中的核心作用。与液体培养基相比，土壤环境中的菌株显著改变了与膜功能（如脂质组成、脂质代谢、细胞脂肪酸合成）、渗透胁迫响应（如多胺或海藻糖合成、钾离子摄取）以及腐胺代谢相关的基因表达，揭示了维罗纳假单胞菌1YdBTEX2在污染土壤中成功定殖的即时响应机制。