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

Abstract

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.

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

“…In contrast, 216 the second functional pathway ( Fig. 3A) 23 , was blocked in iPsvr because it lacked the enzyme 217 2.8.3.6 (highlighted in red in Fig. 3A), and it was therefore disconnected from the main metabolic 218 subnetwork.…”

“…ABSTRACT 23 Understanding the adaptive responses of individual bacterial strains is crucial for microbiome 24 engineering approaches that introduce new functionalities into complex microbiomes, such as 25 xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic 26 reprogramming of the cell, which can be captured by multi-omics, but this data remains 27 formidably challenging to interpret and predict.…”

“…The ability of P. veronii 1YdBTEX2 to grow in contaminated environments 99 makes it a promising candidate for rational complementation of microbial communities in 100 contaminated soils 24 . Based on an available manually curated high-quality genome 23 , we 101 reconstructed the first GEM for P. veronii (iPsvr). Genome-wide transcription changes and 102 exometabolome compounds were measured during growth of P. veronii on toluene, in 103 exponential and in stationary phase.…”

“…Although the 108 temporal variations of the growth rate cannot be predicted using GEMs 25 , we showed that 109 introducing the additional regulatory information from gene expression and metabolomics data 110 into GEMs allows for consistently estimating growth rates at different growth phases. Finally, we 111 incorporated into iPsvr previously published transcriptomics data of P. veronii transits from liquid 112 culture to sand 23 to understand its physiological adaptation in soil. Our work shows strong 113 consistency of model outputs with the experimental data, manifesting that integration of 114 condition-specific omics data into a curated GEM constitutes a major improvement for prediction 115 of metabolic reprogramming during adaptation.…”

“…The experimentally determined maximum specific growth rate of P. veronii strain 1YdBTEX2 in 198 minimal medium with toluene as the sole carbon source was in the range of 0.25 h -1 to 0.35 h -1 . 199 Computational prediction of the growth rate on toluene from the curated iPsvr using experimentally been shown to be the main toluene degradation route in P. veronii 23 . In contrast, 216 the second functional pathway ( Fig.…”