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Thauera is a genus of denitrifying and phosphorus-accumulating bacteria used for removing nitrogen and phosphorus from wastewater. Dissolved oxygen is one of the main factors affecting denitrification and phosphorus accumulation, and there is currently little research on the oxygen sensing regulation mechanism of Thauera bacteria. We studied denitrifying phosphorus accumulation and gene transcription expression of Thauera sp. RT1901 in anaerobic, microaerobic, and aerobic environments and analyzed the protein structure and regulation mode of two oxygen-sensing systems. The results showed that the strain could achieve the similar denitrification and phosphorus accumulation effect in microaerobic environment as in anaerobic environment. Transcriptome analysis showed that as the oxygen concentration continued to rise, the core carbon and phosphorus metabolism pathways of the strain remained unchanged, and the respiratory system shifted from nitrate respiration to aerobic respiration, thereby inhibiting the denitrification pathway. The fumarate nitrate reduction (FNR) protein and FixLJ two-component system performed oxygen sensing to jointly regulate the expression of respiratory genes. The FNR protein formed a dimer in an anaerobic environment, activating denitrification-related genes and inhibiting cytochrome oxidase-related genes. The FixLJ system conducted signal transduction through phosphorylation in a low oxygen environment and activated the transcription of the fixK gene. The FixK protein has a similar structure and function as the FNR protein but is not directly affected by oxygen. These results reveal the oxygen sensing regulation mechanism of Thauera sp. RT1901 in the denitrification and phosphorus accumulation process, providing new insights for further studying the functions of this genus of bacteria in wastewater treatment systems. [Display omitted] • The N and P removal mechanisms of Thauera are evaluated in different oxygen environments. • Thauera regulates the respiratory chain and transport to adapt to oxygen changes. • The FNR protein performs oxygen sensing and regulates in anaerobic and aerobic environments. • The FixLJ system performs oxygen sensing and regulates in microaerobic and aerobic environments. [ABSTRACT FROM AUTHOR]