**Background:** Microalgae are increasingly used for sustainable sewage treatment, offering nutrient removal, heavy metal bioremediation, and potential for valuable co-product recovery. The Tibetan Plateau harbors unique microalgal strains adapted to extreme conditions. Desmodesmus sp. has shown promise in prior studies for nutrient removal and heavy metal adsorption, but the molecular mechanisms underlying its differential response to municipal vs. industrial wastewater were not well understood. This study aimed to characterize transcriptomic and metabolomic differences in a newly isolated Tibetan Desmodesmus sp. when treating simulated municipal sewage (YH_3) versus zinc-copper heavy metal wastewater (YH_4).
**Methods:** The Desmodesmus sp. was isolated from Yamdrok Lake (Tibet, 4300 m) and identified as a new species via polyphasic taxonomy and 18S rRNA sequencing. Cultivation conditions were 25±1°C, pH 7.0–7.5, 3000 Lx, 12h:12h light:dark. Simulated municipal sewage contained glucose, NH₄Cl, KH₂PO₄, and trace elements (COD 400.0±0.5 mg/L, TN 33.0±0.5 mg/L, TP 3.2±0.5 mg/L). Heavy metal wastewater contained CuSO₄·5H₂O (0.037 mg/L) and ZnSO₄·7H₂O (0.044 mg/L). Algal mud from 1 L culture was added to 1 L of each sewage type. Samples were collected at peak treatment efficiency: municipal sewage at 3–5 days (max COD, TN, TP removal), heavy metal sewage at 4–6 hours (max Zn/Cu removal). Three biological replicates per treatment. RNA-seq was performed on Illumina NovaSeq (Q30 >97%, GC ~58%). DEGs were identified with DESeq2 (|log₂FC| >1, adjusted p<0.05). Metabolomics used UHPLC-MS/MS (Orbitrap Q Exactive HF); DAMs defined by VIP>1, p<0.05, FC>2 or <0.5. Co-joint KEGG pathway enrichment analysis was performed on DEGs and DAMs.
**Key Results:** Municipal sewage treatment achieved 96.1% COD removal (day 2), 90.9% TP removal (day 5), and 97.0% TN removal (day 5). Heavy metal treatment achieved 92.5% Zn and 93.5% Cu removal (hour 4). RNA-seq identified 18,505 upregulated and 21,511 downregulated genes in YH_3 vs. YH_4. The most enriched GO terms included ribosome biogenesis, translation, and oxidoreductase activity. KEGG enrichment showed ribosome, photosynthesis, and proteasome pathways as most significant (p<0.01). Metabolomics in positive polarity mode identified 285 DAMs (160 up, 125 down) for YH_3 vs. YH_4; in negative polarity, 285 DAMs (160 up, 125 down). For YH_4 vs. YH_3, positive polarity identified 547 DAMs (267 up, 280 down); negative polarity identified 331 DAMs (144 up, 187 down). Co-joint analysis for YH_3 vs. YH_4 revealed enrichment in photosynthesis, glyoxylate and dicarboxylate metabolism, and carbon fixation in photosynthetic organisms (p<0.01). Key metabolites included ADP (photosynthesis), aspartate and sedoheptulose (carbon fixation), and citrate, succinate, and L-serine (glyoxylate/dicarboxylate metabolism). For YH_4 vs. YH_3, enriched pathways included arginine and proline metabolism, cysteine and methionine metabolism (p<0.01), and carotenoid biosynthesis (p<0.01). Key metabolites: ornithine, D-proline, 5-amino-pentanoate (arginine/proline); L-aspartate, L-serine, 2-oxobutanoate, S-adenosyl-L-methionine (cysteine/methionine); abscisate and abscisic acid glucose ester (carotenoid biosynthesis). S-adenosyl-L-homocysteine was significantly downregulated; 2-oxobutanoate showed both up- and downregulation; abscisic acid glucose ester was significantly upregulated.
**Clinical Implications:** This is a basic science study with no direct clinical applications. However, the findings have implications for environmental biotechnology and wastewater treatment engineering. Understanding the molecular mechanisms of Desmodesmus sp. in different sewage types can guide optimization of microalgae-based treatment systems for complex, mixed wastewater streams. The identification of key metabolites (e.g., citrate, succinate for energy; ABA-GE for heavy metal stress response) provides targets for genetic or process engineering to enhance treatment efficiency and co-product recovery (e.g., amino acids, fatty acids). The study also highlights the importance of harvesting microalgae at optimal treatment times to avoid secondary metabolic processes that may reduce economic value.