Cultivation-medium agitation alters biological and metabolic traits and reshapes the bacterial microbiome of Odontella aurita

Odontella aurita is one of the few microalgal species and the only diatom currently approved as a food supplement in the European Union. This status underscores its relevance as a target for biotechnological innovation and positions it as an emerging model for biological research and metabolic studies. O. aurita is a chain-forming species (cell size approximately 60 μm) rich in carotenoids, lipids, and carbohydrates. To maximize microalgal growth and production and enhancing the synthesis of bioactive compounds, the optimization of large-scale industrial setup is essential. To address this need, the present study investigates the impact of physical disturbance on the growth performance of the O. aurita resource. Non-axenic O. aurita cultures were grown in agitation-based or agitation free cultivation in 6-L tanks under a 12 h: 12 h light: dark photoperiod with a sinusoidal light distribution peaking at 100 μmol m−2 s−1. Bacterial community composition, growth performance, photosynthetic efficiency, and biomass composition were analyzed together with a broad array of metabolites involved in key biochemical pathways, including carotenoids, vitamins, auxin, amino acids, and other polar compounds identified by NMR spectroscopy.Our findings show that agitation-based cultivation profoundly modifies the biological system at multiple levels. Resuspension of O. aurita cells caused by physical disturbance promoted a marked shift in the associated bacterial populations, potentially altering microalga–bacteria interactions, and coinciding with suppressed cell division. Cells that did not undergo division increased in size and exhibited distinct metabolic signatures, particularly in pathways related to sugars, amino acids, and vitamins.