biostudies-literatureMendonca CMNorthwestern UniversityDivision of Chemical, Bioengineering, Environmental, and Transport Systems11041-11052https://www.ebi.ac.uk/biostudies/studies/S-EPMC11210201biostudies-literatureUnknown58(25)Microbial organic matter turnover is an important contributor to the 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 challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in <i>Pseudomonas putida</i>, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our ¹³C-metabolomics data captured substrate carbons into difEnvironmental science & technologyDisproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency.PMC11210201CBET-1653092CBET-2022854Mendonca CMAristilde LZhang LWaldbauer JRfalseDisproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency.Microbial organic matter turnover is an important contributor to the 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 challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in <i>Pseudomonas putida</i>, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our ¹³C-metabolomics data captured substrate carbons into dif2024-01-01T00:00:00Z2024 Jun2025-04-04T21:22:35.105Z2025-04-04T21:22:35.105ZS-EPMC112102013886066810.1021/acs.est.4c01328