Free ammonia (FA) has been recently demonstrated as the primary stress factor suppressing microalgal activities in high-ammonium wastewater. However, its inhibition mechanism and microalgal self-adaptive regulations remain unknown. This study revealed an initial inhibition and subsequent self-adaptation of a wastewater-indigenous Chlorella sp. exposed to FA shock. Mutual physiological and transcriptome analysis indicated that genetic information processing, photosynthesis, and nutrient metabolism were the most influenced metabolic processes. Specifically, for the inhibition behavior, DNA damage was indicated by the significantly up-regulated related genes, leading to the activation of cell cycle checkpoints, programmed apoptosis, and suppressed microalgal growth; FA shock inhibited the photosynthetic activities including both light and dark reactions and photoprotection through non-photochemical quenching; ammonium uptake was also suppressed with the inhibited glutamine synthetase/glutamine alpha-oxoglutarate aminotransferase cycle and the inactivated glutamate dehydrogenase pathway. With respect to microalgal self-adaptation, DNA damage possibly enhanced overall cell viability through reprogramming the cell fate; recovered nutrient uptake provided substances for self-adaptation activities including amino acid biosynthesis, energy production and storage, and genetic information processing; elevated light reactions further promoted self adaptation through photodamage repair, photoprotection, and antioxidant systems. These findings enrich our knowledge of microalgal molecular responses to FA shock, facilitating the development of engineering optimization strategies for the microalgal wastewater bioremediation system.
