2.5 Statistical analysis
Physiological data were analyzed using the SPSS 17.0 software (SPSS
Inc., Chicago, IL, USA). Significant differences among the means of
different treatments were determined by Tukey’s multiple range tests
after conducting tests of homogeneity for variances. Differences were
considered statistically significant at the p < 0.05
level. To assess alpha-diversity, communities were rarified to 11 000
(bacteria) and 10 000 (fungi) sequences per sample. Alpha-diversity
indexes (Ace index and Sobs index) were calculated using QIIME (Caporaso
et al., 2010). The significances of differences among treatments were
assessed using the Welch’s t-test. Similarities and differences arising
from microbiomes of different soil samples were visualized with Circos
(Krzywinski et al., 2009). Bray-Curtis distances between samples were
used for principal coordinate
analysis (PCoA) to assess the major variance components of the
beta-diversity. Permutational
multivariate analysis of variance (PERMANOVA) was used to evaluate group
differences. Discriminant taxa were
significantly retrieved by linear discriminant analysis (LDA) effect
size (LEfSe) for bulk-soil and
rhizosphere-microbial communities
(Segata et al., 2011).