Treating wastewater using purple non-sulfur bacteria (PNSB) is an environmentally friendly technique that can simultaneously remove pollutants and lead to the accumulation of high-value cell inclusions. However, no PNSB system for treating heavy oil refinery wastewater (HORW) and recovering high-value cell inclusions has yet been developed. In this study, five batch PNSB systems dominated by Rhodopseudomonas were used to treat real HORW for 186 d. The effects of using different hydraulic retention times (HRT), sludge retention times (SRT), trace element solutions, phosphate loads, and influent loads were investigated, and the bacteriochlorophyll, carotenoid, and coenzyme Q10 concentrations were determined. The community structure and quantity of Rhodopseudomonas in the systems were determined using a high-sequencing technique and quantitative polymerase chain reaction technique. The long-term results indicated that phosphate was the limiting factor for treating HORW in the PNSB reactor. The soluble chemical oxygen demand (SCOD) removal rates were 67.03% and 85.26% without and with phosphate added, respectively, and the NH4+-N removal rates were 32.18% and 89.22%, respectively. The NO3−-N concentration in the effluent was stable at 0–3 mg/L with or without phosphate added. Adding phosphate increased the Rhodopseudomonas relative abundance and number by 13.21% and 41.61%, respectively, to 57.35% and 8.52 × 106 gene copies/μL, respectively. The SRT was the limiting factor for SCOD removal, and the bacteria concentration was the limiting factor for nitrogen removal. Once the inflow load had been increased, the total nitrogen (TN) removal rate increased as the HRT increased. Maximum TN removal rates of 64.46%, 68.06%, 73.89%, 82.15%, and 89.73% were found at HRT of 7, 10, 13, 16, and 19 d, respectively. The highest bacteriochlorophyll, carotenoid, and coenzyme Q10 concentrations were 2.92, 4.99, and 4.53 mg/L, respectively. This study provided a simple and efficient method for treating HORW and reutilizing resources, providing theoretical support and parameter guidance for the application of Rhodopseudomonas in treating HORW.
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