3.1. Effects of Each Treatment on the Composition and Content of Phospholipid Fatty Acids
Altogether, 20 kinds of phospholipid fatty acids were checked from the soil samples treated by the different rotation and fertilizer treatments. There were seven kinds of phospholipid fatty acids among the 20 kinds of phospholipid fatty acids with significant effects with regard to the rotation treatment or interaction between rotation treatment and fertilizer treatment. From
Table 3, we can see that seven kinds of phospholipid fatty acids were mainly detected in this study, in which 16:0 (Gram-positive bacteria) had the maximum content, accounting for 11.6–12.7% of the total phospholipid fatty acids. These seven kinds of phospholipid fatty acids belonged to Gram-positive bacteria, Gram-negative bacteria, AM Fungi, Actinomycetes, and other bacteria.
The rotation treatment had a significant effect on the content of a15:0, 16:0, 16:1ω5c, and 18:0 at p ≤ 0.01, had a significant effect on 17:1 ω 7c and 10Me18:0 at p ≤ 0.05, and did not have a significant effect on i16:0. The fertilizer treatment had no significant effect on the content of the above phospholipid fatty acids, there were significant effect on the content of i16:0 at p ≤ 0.05 in the interaction between rotation treatment and fertilizer treatment, no significant differences were observed between the others as a result of the interaction between the treatment of rotation and fertilizer.
For a15:0, soybean continuous cropping with chemical fertilizer applied resulted in significantly higher numbers than that maize continuous cropping with organic fertilizer and chemical fertilizer applied. For another Gram-positive bacteria (i16:0), there was significant interaction between fertilizer and cropping system (p = 0.047). For 17:1 ω 7c, continuous cropping of maize without fertilizer was remarkably higher than soybean continuous cropping with organic fertilizer and without fertilization. Cropping system had a significant effect on its content at 0.05 level (p = 0.018). Cropping system had an extremely significant influence on 16:1 ω 5c (AM Fungi (Arbuscular Mycorrhizal Fungi)) at the 0.01 level (p = 0.000); its numbers were significantly lower in soybean continuous cropping than maize continuous cropping and soybean-maize rotation.
The content of 10Me18:0 presented a significant difference under the SM + OF, which displayed significantly higher content than all of the other treatments, and there was no significant difference between the other treatments. The 18:0 displayed a significant difference under the CS + OF, CS + NP, and CS + 0, although there was no significant difference observed between CS + OF, CS + NP, and CS + 0, all of which displayed significantly higher content than all the other treatments.
The rotation treatment had a significant effect on the content of Gram-positive bacteria (G+) and the other bacteria at
p ≤ 0.01; had a significant effect on Gram-negative bacteria (G-), fungi, and fungi/bacteria at
p ≤ 0.05; but did not have a significant effect on Actinomycetes. The fertilizer treatment had no significant effect on the content of the above phospholipid fatty acids, only the content of Gram-positive bacteria (G+) showed significant differences at
p ≤ 0.05 in the interaction between rotation treatment and fertilizer treatment.
Table 4 shows that bacteria accounted for 69% to 71% of the total amount of soil microorganisms, and thus represented the main component of the soil microorganisms. While fungi only accounted for about 3% of the total amount of microorganisms, other bacteria accounted for 8.1–9.9% of the total amount. Cropping system had a significant effect on the composition of the soil microbial community and had a significant effect on Gram-positive bacteria (
p = 0.008) and other bacteria (
p = 0.006). For Gram-positive bacteria, there was an obvious interaction between fertilizer and farming system (
p = 0.034).
Analysis of variance for the fertilizer treatment showed that the content of Gram-negative bacteria (G-) was significantly affected by fertilizer application under the condition of continuous maize cropping system at the 0.01 level. The content of Gram-positive bacteria (G+) was significantly affected by fertilizer application under the condition of soybean-maize rotation system at the 0.01 level (
Table 5). Under the condition of continuous maize cropping system, the content of Gram-negative bacteria (G-) treated by organic fertilizer and chemical fertilizer application was significantly higher than that of no fertilizer treatment at the level of 0.01, and there was no significant difference between the organic fertilizer and chemical fertilizer application treatments. Under the condition of the soybean-maize rotation system, the content of Gram-positive bacteria (G+) treated by organic fertilizer application and no fertilizer was significantly higher than that of chemical fertilizer application at the 0.01 level, and there was no significant difference between the organic fertilizer application and no fertilizer.
3.2. Principal Component Analysis of Microbial Fatty Acids in Soil by Each Treatment
The principal component analysis of the microbial fatty acids in soil is presented in
Figure 1, where explanation variances of the first principal component (PC1) and the second principal component are 34.76% and 28.98%, respectively (
Figure 1). Indeed, PC1 is highly related with i17:0, a17:0, and i15:0, which all belong to Gram-positive bacteria, and their component matrix coefficients are 0.932, 0.911, and 0.876, respectively (
Figure 1,
Table 6). Meanwhile, PC2 displays the more obvious correlations with 18:1 ω 9c, cy17:0 ω 7c, and 16:1 ω 5c, with corresponding component matrix coefficients of 0.866, 0.846, and 0.802, respectively (
Figure 1,
Table 6). However, there are some lower correlations between PC1 and 18:0, 16:0, and 17:1 ω 7c, which have corresponding component matrix coefficients of −0.053, −0.030, and −0.080, respectively. Moreover, the component matrix coefficients of i17:0, a17:0, and 10Me16:0 to PC2 are also lower, with corresponding values of 0.064, 0.054, and 0.062, respectively (
Figure 1,
Table 6).