Mechanistic Model of B12-based Syntrophy Between Thalassiosira pseudonana and Ruegeria pomeroyi

Vitamin B₁₂ auxotrophy among diatoms is considered an important mechanism governing interactions with bacteria in the Roseobacter clade. Under vitamin B₁₂ (cobalamin) starvation conditions, a co-culture of the B₁₂-producer Ruegeria pomeroyi DSS-3 and the B₁₂-auxotroph Thalassiosira pseudoanana CCMP 1335 will exhibit syntrophic growth. We re-constructed a genome-scale metabolic model of DSS-3 that contains 1,688 reactions and 923 metabolites, representing the metabolic activity of 1,301 genes (~30% of the genome). The DSS-3 model was paired with a genome-scale metabolic model of CCMP 1335 (previous work) to simulate cross-feeding in batch culture using dynamic Flux Balance Analysis with constraints derived from RNAseq data. We assumed that each organism takes up nutrients from and excretes metabolites into its own extracellular space, which impacts the partner organism’s extracellular space in the next time step. This simulation confirmed published predictions made solely from the analysis of transcripts, including production of 2,3-dihydroxypropane-1-sulfonate (DHPS) by CCMP 1335 in exchange for cobalamin. Metabolic transfer between trophic levels remain difficult to measure because these fluxes are likely ephemeral, involve a diverse assortment of molecules, and occur over microscopic distances. Constraint-based metabolic modeling can be used to simulate fluxes in sequenced marine organisms, giving us the ability to integrate a wealth of molecular information to effectively develop and test systems-level hypotheses.