No abstract

Highlights d Bacillus and Pseudomonas interaction ranges from antagonism to co-existence d Bacillaene from Bacillus is a bacteriostatic that targets FusA of Pseudomonas d GlpK mutations in Bacillus confer unspecific antimicrobial resistance

Summary Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan‐genome analysis has revealed that 30% of genes belong to the core‐genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA‐seq analysis compared the short‐ and long‐term responses of the toluene‐sensitive KT2440 strain and the highly tolerant DOT‐T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT‐T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT‐T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy‐intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT‐T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT‐T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.

Summary P seudomonas putida  BIRD‐1 has the potential to be used for the industrial production of butanol due to its solvent tolerance and ability to metabolize low‐cost compounds. However, the strain has two major limitations: it assimilates butanol as sole carbon source and butanol concentrations above 1% (v/v) are toxic. With the aim of facilitating BIRD‐1 strain design for industrial use, a genome‐wide mini‐Tn5 transposon mutant library was screened for clones exhibiting increased butanol sensitivity or deficiency in butanol assimilation. Twenty‐one mutants were selected that were affected in one or both of the processes. These mutants exhibited insertions in various genes, including those involved in the TCA cycle, fatty acid metabolism, transcription, cofactor synthesis and membrane integrity. An omics‐based analysis revealed key genes involved in the butanol response. Transcriptomic and proteomic studies were carried out to compare short and long‐term tolerance and assimilation traits. P seudomonas putida initiates various butanol assimilation pathways via alcohol and aldehyde dehydrogenases that channel the compound to central metabolism through the glyoxylate shunt pathway. Accordingly, isocitrate lyase – a key enzyme of the pathway – was the most abundant protein when butanol was used as the sole carbon source. Upregulation of two genes encoding proteins PPUBIRD1_2240 and PPUBIRD1_2241 (acyl‐CoA dehydrogenase and acyl‐CoA synthetase respectively) linked butanol assimilation with acyl‐CoA metabolism. Butanol tolerance was found to be primarily linked to classic solvent defense mechanisms, such as efflux pumps, membrane modifications and control of redox state. Our results also highlight the intensive energy requirements for butanol production and tolerance; thus, enhancing TCA cycle operation may represent a promising strategy for enhanced butanol production.