TITLE: Disproportionate carbon dioxide efflux in bacterial metabolic pathways for different organic substrates leads to variable contribution to carbon use efficiency
—ABSTRACT: Microbial organic matter turnover is an important contributor to terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenged proposals of CUE dependence on oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variable CUE for organic substrates. We performed a multi-omics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C metabolic flux analysis revealed three-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis determined enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided evaluation for the conversion of accessible organic matter to CO2 efflux. [Link to Open Access Article]