Single-cell metabolic flux analysis reveals coexisting optimal sub-groups, cross-feeding, and mixotrophy in a cyanobacterial population

TL;DR

This study uses single-cell isotope measurements and modeling to uncover metabolic diversity, cross-feeding, and mixotrophy in a cyanobacterial population, revealing how individual behaviors shape collective phenotypes.

Contribution

It introduces a novel integration of SIMS data with statistical and constraint-based models to analyze single-cell metabolism and population heterogeneity.

Findings

Identification of two distinct metabolic sub-groups within the population.

Evidence of metabolic exchange and partial heterotrophy among cells.

Mixotrophic cells exhibit the fastest growth rates.

Abstract

We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptake measurements of Synechocystis sp. PCC6803 with a statistical inference protocol based on Liebig's law of the minimum, the maximum entropy principle, and constraint-based modeling. We find the population is structured in two metabolically distinct clusters: cells optimizing carbon yield while excessively turning over nitrogen, and cells which act reciprocally, optimizing nitrogen yield and excessively turning over carbon. This partition enables partial heterotrophy within the population via metabolic exchange, likely in the form of organic acids. Exchange increases the feasible metabolic space, and mixotrophic cells achieve the fastest growth rates. Metabolic flux analysis at the single-cell level reveals heterogeneity in carbon fixation rates, Rubisco specificity, and nitrogen assimilation. Our results provide a necessary foundation for understanding how population level phenotypes arise from the collective contributions of distinct individuals.