Microalgae endemic to desert ecosystems possess exceptional stress-resistance traits; however, the physiological and molecular drought-adaptation mechanisms of desert-dwelling Chlorella remain largely uncharacterized. Herein, we combined physiological–biochemical assays, ultrastructural observation, transcriptomics and metabolomics to dissect drought responses in Taklamakan-desert-origin Chlorella sp. under polyethylene glycol 6000 (PEG-6000)-simulated mild (10%), moderate (20%), and severe (30%) drought stress, with mechanistic focus on moderate-drought conditions. Moderate drought repressed algal biomass (−26.32%), chlorophyll a (−24.40%), maximum photosystem II quantum yield (Fv/Fm, −16.55%) and effective quantum yield of photosystem II (ΦPSII, −24.35%). Malondialdehyde (MDA) accumulated (+50.69%), alongside elevated activities of superoxide dismutase (SOD, +156.74%) and catalase (CAT, +11.61%). Compatible solutes, including proline, soluble sugars, total protein and total lipid, increased significantly by 39.00%, 39.36%, 26.35% and 23.06%, respectively (p < 0.05). Moderate drought triggered cell swelling, partial cell-wall rupture and prominent enlargement of intracellular starch granules and lipid droplets. Transcriptomic profiling demonstrated up-regulation of transcription–translation and DNA-repair machinery, ATP-binding cassette (ABC) transporters, abscisic acid (ABA)/jasmonic acid (JA) signaling, and biosynthetic pathways for protective metabolites, whereas catabolic pathways and mitogen-activated protein kinase (MAPK) signaling were suppressed. Untargeted metabolomics further validated accumulation of trehalose, stress-protective amino acids, vitamins and functional lipids, while chloroplast-membrane-related metabolites and catabolic intermediates declined. This multi-omics study systematically reveals physiological and molecular regulatory cascades underlying drought tolerance in desert Chlorella sp., providing candidate genes and metabolites to support microalgal resource exploitation for arid-zone applications.

Desert microalgae possess a remarkable tolerance to extreme abiotic stresses; however, the molecular mechanism underlying their stress adaptation and metabolite accumulation remains poorly understood. In the present study, desert Chlorella sp. TLD 6B was exposed to different concentrations of NaCl to assess changes in the soluble sugar and lipid content, as well as transcriptome profiles. The regulatory role of malate synthase 1 (MS1) in modulating soluble sugar and lipid accumulation was further investigated in desert Chlorella under salinity conditions. The results revealed that salt stress markedly elevated soluble sugar and lipid levels in desert Chlorella, while strongly upregulating the transcript expression and enzymatic activity of MS1. Under salt stress, the overexpression of MS1 in desert Chlorella increased the soluble sugar content by 46.49% and the lipid content by 43.87%. The ectopic overexpression of desert Chlorella MS1 in Arabidopsis enhanced salt and drought tolerance without impacting normal plant growth. Mechanistically, MS1 activation modulates metabolic fluxes of the glyoxylate cycle (GAC) and TCA, thereby promoting soluble sugar and lipid accumulation in Chlorella. These findings advance the understanding of GAC-governed sugar and lipid accumulation in desert Chlorella under salt stress, laying a theoretical foundation for the exploitation of desert microalgae resources in biomass energy development.