The circadian clock mediates metabolic functions of plants and rhythmically shapes structure and function of microbial communities in the rhizosphere. However, it is unclear how the circadian rhythm of plant hosts regulates changes in rhizosphere bacterial and fungal communities and nutrient cycles. In the present study, we measured diel changes in the rhizosphere of bacterial and fungal communities, and in nitrogen (N) and phosphorus (P) cycling in 20-year-old tea plantations. The fungal communities were more stable in their responses to circadian changes than bacterial communities in the rhizosphere of the cultivars LJ43 and ZC108. Nevertheless, fungal genera with circadian rhythms were more numerous and had a higher abundance at midnight. Organic P and N mineralization in the rhizosphere was more intensive in LJ43 under day–night alterations, while inorganic N and P cycling was more easily affected by circadian rhythms in ZC108. The rhizosphere denitrification encoded by the genes AOA and AOB was intensive in the morning, irrespective of tea cultivar. Genes related to rhizosphere N fixation (nifH) and denitrification (nosZ and nirK) expressed at greater levels in ZC108, and they reached a peak at midnight. Moreover, the diel rhythm of rhizosphere microbial communities in ZC108 largely regulated dial changes in N and P cycling. These results suggested that the bacterial and fungal communities in the rhizosphere respond differently to circadian rhythms, and they vary between tea cultivars. The timing of bacterial and fungal cycling largely regulates rhizosphere N and P cycling and their ecological functions.

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