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Background Schizochytrium  sp. is a marine heterotrophic protist and an important sustainable resource for high value-added docosahexaenoic acid in the future. The production of different phenotypes during the continuous subculture of  Schizochytrium  sp. results in a serious reduction in lipid yield and complicates the used of this strain in scientific research and industrial production. Hence, obtaining an improved understanding of the phenotypic differences and molecular mechanisms underlying the cell-to-cell heterogeneity of  Schizochytrium  sp. is necessary. Results After continuous culture passage,  Schizochytrium  sp. H016 differentiated into two subpopulations with different morphologies and showed decreased capacity for lipid production. The presence of cell subpopulations with degraded lipid droplets led to a substantial decrease in overall lipid yield. Here, a rapid screening strategy based on fluorescence-activated cell sorting was proposed to classify and isolate subpopulations quickly in accordance with their lipid-producing capability. The final biomass and lipid yield of the subpopulation with high cell lipid content (i.e., H016-H) were 38.83 and 17.22 g/L, respectively, which were 2.07- and 5.38-fold higher than those of the subpopulation with low lipid content (i.e., H016-L), respectively. Subsequently, time‑resolved transcriptome analysis was performed to elucidate the mechanism of phenotypic heterogeneity in different subpopulations. Results showed that the expression of genes related to the cell cycle and lipid degradation was significantly upregulated in H016-L, whereas the metabolic pathways related to fatty acid synthesis and glyceride accumulation were remarkably upregulated in H016-H. Conclusion This study innovatively used flow cytometry combined with transcriptome technology to provide new insights into the phenotypic heterogeneity of different cell subpopulations of  Schizochytrium  sp. Furthermore, these results lay a strong foundation for guiding the breeding of oleaginous microorganisms with high lipid contents.

New insights into phenotypic heterogeneity for the distinct lipid accumulation of Schizochytrium sp. H016