Characterization and genome-scale metabolic modeling of catechol-degrading Pseudomonas fluorescens isolated from a petroleum hydrocarbon-impacted site

Abstract

Pseudomonas fluorescens is a candidate for efficient petroleum hydrocarbons (PHC) biodegradation. In this work, a P. fluorescens strain was isolated from a local PHC-impacted site. To investigate its PHC biodegradation performance, catechol, an important metabolic intermediate during monoaromatic hydrocarbon biodegradation, was chosen as the sole carbon source. A set of experiments based on a 23 factorial design was undertaken to investigate how nitrate, sulfate, and phosphate ions affect catechol biodegradation by the isolated P. fluorescens strain. The experimental results were subjected to ANOVA. Maximum specific catechol degradation rates (the response) were estimated by a three-parameter logistic model to evaluate bioremediation performance. ANOVA results suggest introducing nitrate ions alone may lead to poorer bioremediation performance, introducing sulfate ions alone does not affect bioremediation performance, but supplementing with nitrate and sulfate ions together can enhance bioremediation performance. P. fluorescens was also shown to survive under sulfur-limited conditions. Injecting phosphate ions also led to better bioremediation performance. To gain extensive and systematic knowledge of P. fluorescens, the first genome-scale metabolic model (GSMM) for P. fluorescens was reconstructed, termed lCW1057. The model was validated by in vitro growth data. The periplasmic compartment was constructed to better represent the proton gradient profile. The reconstructed proton transport chain has a P/O ratio of 11/8. Flux balance analysis (FBA) was performed to simulate the whole-cell metabolic flow. The simulation results suggested the β-ketoadipate pathway is involved in catechol metabolism by P. fluorescens while the uptake of oxygen is mandatory for cleavage of catechol’s aromatic ring. The Entner-Doudoroff (ED) pathway was involved in glycolysis for P. fluorescens. Moreover, nitrates can be used as the terminal electron acceptor to support P. fluorescens growth under anaerobic condition.