Objectives We studied the effects of application ratios of chemical and organic fertilizers on the structure and diversity of rhizosphere bacterial and fungal communities using photo-assimilated carbon, in order to understand the main factors causing the variation of microbial communities.

Methods A pot experiment was carried out in the greenhouse of Taoyuan Agricultural and Ecological Experimental Station of Chinese Academy of Sciences, Hunan, China. The oilseed rape cultivar for the test was Xiangzayou 6, and the soil was red soil. Under equal inputs of N, P and K, chemical and organic fertilizer N ratio of 100∶0 (CK), 3∶1 (OF25), 1∶1 (OF50), 1∶3 (OF75), 0∶100 (OF100) were made as treatments. Since the 40 days of transplanting, the test soil was labelled with ¹³CO₂ for 20 consecutive days. Then the rhizosphere soil samples were collected for determination of phospholipid fatty acids (PLFA) and the ¹³C values using gas chromatography-combustion-isotope ratio mass spectrometry, the microbial species and the relative abundance were then acquired. The sum of single ¹³C-PLFA was defined as the total microorganism amount.

Results A total of 12 bacteria and 3 fungi were identified using photo-assimilated carbon, where in the bacteria were gram-positive (G⁺) a15:0, i17:0, and gram-negative (G⁻) 2OH 14:0, 3OH 14:0, cy17:0; 14:0, 16:0, 15:0, 18:0, 19:0, 20:0, 17:0, and the fungi were 18:1w9tans, 18:2w6c, and 18:1w9c. The contents of ¹³C labelled G⁺ bacteria and fungi PLFAs in treatments OF75 and OF100 were not significantly different from those in CK, while the G⁻ bacteria PLFA contents were 36.41% and 62.03% higher than those in CK, respectively. ¹³C-fungi and ¹³C-G⁺ were the main communities utilizing the photo-assimilated carbon, and with the increase of the proportion of organic fertilizers, the relative abundance of ¹³C-G⁺ bacteria increased and that of ¹³C-fungi decreased; the relative abundance of ¹³C-G⁻ bacteria increased and relative abundance of G⁺ bacteria decreased. Rhizosphere soil organic carbon, total P, total N, and total amino acids significantly affected the structures of microbial communities, whereas the amino acid contents in root excrete was significantly and positively correlated with the diversity of ¹³C-microorganisms only.

Conclusions The ratio of chemical fertilizer to organic fertilizer caused changes in the organic carbon and total nitrogen contents in rhizosphere soil, as well as the amino acid contents in root excretes, which in turn affected the composition and diversity of microbial communities utilizing photo-assimilated carbon in the rhizosphere soil. When the ratio of chemical and organic fertilizers reached 1∶3, the content and diversity of characteristic microorganisms in the rhizosphere soil of oilseed rape were significantly higher than that under chemical fertilizer alone, indicating the more friendly micro-ecological environment for microorganisms under this ratio.