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

• Published in: PloS one Vol. 11; no. 11; p. e0165850
• Main Authors: Morales, Marian, Sentchilo, Vladimir, Bertelli, Claire, Komljenovic, Andrea, Kryuchkova-Mostacci, Nadezda, Bourdilloud, Audrey, Linke, Burkhard, Goesmann, Alexander, Harshman, Keith, Segers, Francisca, Delapierre, Fabien, Fiorucci, Damien, Seppey, Mathieu, Trofimenco, Evgeniya, Berra, Pauline, El Taher, Athimed, Loiseau, Chloé, Roggero, Dejan, Sulfiotti, Madeleine, Etienne, Angela, Ruiz Buendia, Gustavo, Pillard, Loïc, Escoriza, Angelique, Moritz, Roxane, Schneider, Cedric, Alfonso, Esteban, Ben Jeddou, Fatma, Selmoni, Oliver, Resch, Gregory, Greub, Gilbert, Emery, Olivier, Dubey, Manupriyam, Pillonel, Trestan, Robinson-Rechavi, Marc, van der Meer, Jan Roelof
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 03.11.2016; Public Library of Science (PLoS)
• Subjects: Adaptation; Analysis; Anopheles; Aromatic hydrocarbons; Bacteria; Benzene; Biodegradation; Biodegradation, Environmental; Bioinformatics; Biology and Life Sciences; Bioremediation; Cellular stress response; Chemical industry; Chemotaxis; Degradation; Ecology; Efflux; Ethylbenzene; Evolution; Fatty acids; Gene clusters; Gene expression; Gene Expression Regulation, Bacterial - drug effects; Genes; Genome, Bacterial - genetics; Genomes; Genomics; Hydrocarbons; Inoculation; Life sciences; Lipid composition; Lipid metabolism; Metabolism; Nucleotide sequence; Osmotic stress; p-Xylene; Paraxylene; Physical Sciences; Physiology; Pollutants; Pollution; Potassium; Pseudomonas; Pseudomonas - drug effects; Pseudomonas - genetics; Pseudomonas - metabolism; Pseudomonas putida; Pseudomonas veronii; Putrescine; Research and Analysis Methods; Restoration; Sediment pollution; Soil contamination; Soil Pollutants - isolation & purification; Soil Pollutants - metabolism; Soil Pollutants - toxicity; Soil pollution; Soils; Synthesis; Toluene; Toluene - isolation & purification; Toluene - metabolism; Toluene - toxicity; Transcription; Transcription (Genetics); Trehalose; Xylene
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0165850

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.