The effectiveness of rural domestic sewage treatment significantly impacts the living environment and quality of life of residents. A rural domestic sewage treatment facility in Yuncheng City, Shanxi Province, China, was utilized to investigate the operational effect and CO2 flux of a sewage treatment process. This process involved anaerobic pretreatment, followed by the application of two sets of constructed wetlands (CWs) for advanced treatment. One group of CWs incorporated local folk-story elements, and the landscape of ‘Carps Leaping over the Dragon Gate’ was created through plants collocation (CW1). The other group adopted a regular row design (CW2). The results indicated that the removal rates for chemical oxygen demand (COD) (72.41–92.91%), ammoniacal nitrogen (NH4+-N) (94.80–99.33%), and total phosphorus (TP) (27.56–67.62%) in CW1 were comparable to those in CW2. However, the removal rate of total nitrogen (TN) (51.64–85.59%) was higher than that in CW2. Meanwhile, the substrate CO2 flux in CW1 (145.68–1637.11 mg/m2/h) was slightly higher than that in CW2 (131.22–1597.22 mg/m2/h). The decline in the daily average temperature, which caused reduced microbial activity and plant wilting, was the primary factor contributing to the changes in the pollutant removal rate and CO2 flux. Pennisetum giganteum z. x. lin and Arundo donax L. var. versicolor Stokes grew in clusters, and the root biomass was large, enabling them to secrete more organic compounds to enhance the activity of rhizosphere microorganisms. Variations in plant species led to different rates of root carbon fixation, which, in turn, affected the CO2 emissions from the CW substrate layer. Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Bacteroidota were the dominant phyla and could utilize the nutrients and oxygen transported by plant roots to enhance nitrification and denitrification processes. This study provides a reference for the promotion of domestic sewage treatment in rural areas of China.
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