Integrated omics analysis reveals reorganization of nitrogen and lipid metabolism in a toluene-degrading bacterium in the gas phase

Abstract

Gas-phase bioprocesses, in which microbial cells are immobilized on solid carriers exposed to the gas phase, enable efficient conversion of poorly water-soluble compounds for biodegradation and bioproduction. However, operation without a surrounding bulk aqueous medium can constrain the replenishment of water and nonvolatile nutrients. The metabolic mechanisms that sustain cellular activity in these low-water environments remain largely unknown. Here, we elucidated the metabolic alterations in the highly adhesive bacterium Acinetobacter sp. Tol 5 degrading toluene in the gas and aqueous phases. Polyurethane carriers bearing cells from independent cultures were assigned to the gas phase or to two aqueous media, nitrogen-depleted basal salt medium and phosphate-buffered saline, so that the conditions differed only in phase and nutrient availability. In cells actively degrading toluene, integrated metabolomics, lipidomics, and transcriptomics (97 metabolites, 108 lipids, and 3,899 genes) revealed a metabolic state specific to the gas phase. Under gas-phase conditions, amino acid and nucleotide degradation was enhanced while the intracellular glutamate pool was maintained at a high level, and citrulline specifically accumulated. Membrane lipids were remodeled, and the storage lipid triacylglycerol was consumed, suggesting that it serves as an endogenous carbon and energy source and may also contribute to metabolic water production under nutrient- and water-limited gas-phase conditions. These findings highlight nitrogen metabolism and lipid mobilization as features of gas-phase adaptation, providing a rational basis for designing robust gas-phase bioprocesses and selecting suitable microbial chassis.