Kratzl, F. P. | bioRxiv Science

bioRxiv2026

Organizing principles in the Nitrogen-Carbon Landscape of Marine Heterotrophic Bacteria

Marine microbes metabolize a wide range of carbon and nitrogen sources, shaping global biogeochemical cycles. Despite being crucial at the global scale, the coupling between carbon and nitrogen remains poorly understood at the level of individual metabolites and bacteria. By phenotyping a library of marine heterotrophic bacteria across increasingly complex carbon and nitrogen sources, we generated a snapshot of this coupling. Growth phenotypes were weakly explained by phylogeny, but could be organized around substrate properties, including C:N stoichiometry and degree of reduction. Beyond explainable average trends along these axes, different strains displayed significant variability. For some bacteria, nitrogen use efficiency was associated with ammonium secretion, consistent with their role in ecological interactions. Furthermore, nonlinearities emerged in how yields depend on combinations of resources, such as mixtures of amino acids and dipeptides. These organizing principles may help understand the ecological role of marine heterotrophic bacteria and parametrize models of biogeochemical cycles.

systems biology↗

bioRxiv2026

Reconstructing heterogeneous metabolic trajectories of E. coli diauxie via a dynamical Maximum Entropy Principle

The glucose-acetate diauxic shift in E. coli is classically described as an abrupt, population-wide switch from glucose to acetate consumption. Recent experiments challenge this view, revealing a robust intermediate regime of co-consumption whose single-cell basis remains unresolved: does it reflect coexisting specialized subpopulations, or genuine mixed metabolic states within individual cells? We first develop a two-state consumer-resource model in which cells optimally grow on either glucose or acetate, and show that observed co-consumption trajectories cannot be decomposed into convex combinations of the two subpopulations -- ruling out discrete metabolic states as a sufficient explanation. Physico-chemical constraints of the metabolic network instead enforce genuine single-cell co-consumption across a continuous spectrum of phenotypes. To resolve this, we apply a dynamical maximum entropy (maximum caliber) framework constrained by batch and chemostat experiments, inferring time-resolved distributions of metabolic fluxes that naturally predict a continuum of single-cell phenotypes spanning glucose overflow, mixed substrate utilization, and acetate consumption -- revealing co-consumption as a dominant, persistent feature of single-cell metabolism around the switch rather than an artifact of population averaging. Finally, we formulate a continuous consumer-resource model over metabolic state space, in which selection, phenotypic diffusion, and moving metabolic boundaries driven by environmental feedback reproduce single-cell co-consumption trajectories and complex dynamical trends inaccessible to discrete models. Together, our results recast diauxic adaptation as a continuous redistribution of single-cell metabolic states rather than a discrete switch.

systems biology↗