Mineral fertilisers differ in changing soil properties, and revealing how the rhizosphere and non-rhizosphere respond could provide a robust assessment of fertiliser regimes. Rhizosphere and non-rhizosphere soils were sampled from five fertilisation treatments in a long-term (24 year) experiment. Enzyme activities and total phospholipid fatty acids (PLFA) content in the rhizosphere soil were 85.8% and 51.3% higher than in the non-rhizosphere soil, respectively. Fertilisation increased enzyme activities, especially the N-cycling enzyme β-1,4-N-acetylglucosaminidase in NP fertilised soil (1.5 and 2.5 times for rhizosphere and non-rhizosphere soil, respectively). The PLFA composition indicated that fungi dominated in the rhizosphere fertilised with P, whereas bacteria were more common in the non-rhizosphere soil. The PLFA contents and enzyme activities in the rhizosphere of P-fertilised plants were lower than those in the non-rhizosphere soil because P availability was lower in the rhizosphere. The redundancy analysis showed that the microbial community in the rhizosphere soil was different from that of the non-rhizosphere soil, mainly because there were differences in the 15:1ω6c and 16:0. Long-term (24 year) fertilisation strongly increased nutrient contents, and microbial biomass and activity in paddy soil. It is advisable to apply P fertiliser in the root zone to increase fertiliser use efficiency.
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