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bioRxiv · 10.64898/2026.10.15.759342

Experimental trophic flexibility guides a compartmentalized genome-scale model of red microalgae Galdieria sulphuraria

Pentjuss, A.·Kolesovs, S.·Grube, M.·Scerbaka, R.·Svirksts, K.·Stalidzans, E.·Vigants, A.·Smetana, S.·Pleissner, D.
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Abstract

The thermoacidophilic red microalga Galdieria sulphuraria combines broad organic-carbon utilization with biotechnological robustness. We integrated cultivation data for strain SAG 107.79 with an organelle-resolved genome-scale metabolic model describing autotrophic, mixotrophic and heterotrophic metabolism. Heterotrophic cultures produced 2.29, 2.03 and 2.14 g L-1 biomass on glucose, xylose and their mixture, respectively, while mixed-sugar cultures consumed glucose before xylose. Biomass composition was similar under mixotrophy and heterotrophy, and stationary-phase glucose consumption supported a non-growth-associated maintenance demand of 1.7 mmol ATP gDW-1 h-1. These measurements informed trophic-state-specific biomass objective functions. The final model contains 2,487 reactions, 2,270 compartment-specific metabolites and 1,050 genes. The model reproduced the experimentally scored growth phenotypes, highlighted polyol-associated product capacity under heterotrophy and scored 90% in the archived MEMOTE report. To our knowledge, this is the first experimentally based, organelle-resolved genome-scale metabolic model for G. sulphuraria, providing a quantitative framework linking trophic state and substrate identity with carbon use, flux flexibility and product capacity. A user-friendly supplementary package provides the executable SBML model, modular biomass resources, reproducible scripts, quality reports and underlying experimental data.

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Pentjuss, A., Kolesovs, S., Grube, M., Scerbaka, R., Svirksts, K., Stalidzans, E., Vigants, A., Smetana, S., Pleissner, D.. 2026-10-16. Experimental trophic flexibility guides a compartmentalized genome-scale model of red microalgae Galdieria sulphuraria. https://doi.org/10.64898/2026.10.15.759342

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