Canoco 5.0 for windows

Statistical comparisons of metabolic gene abundances were conducted by SPSS 19.0 for Windows (IBM, Chicago, IL, USA) using nonparametric one-way ANOVA and Kruskal-Wallis Multiple Comparison Z test with Bonferroni adjustment. Redundancy analysis (RDA) were conducted by CANOCO 5.0 for Windows (Microcomputer Power Inc., Ithaca, NY).

Canonical correspondence analysis (CCA) was performed using CANOCO 5.0 for Windows (Microcomputer Power, Ithaca, NY, USA) to characterize the effect of measured soil properties on the composition of bacteria communities carrying cbbL gene. Significant differences in community composition were tested by permutational Two-Way analysis of variance or multivariate analysis of variance (MANOVA) implemented in PAST (Hammer et al., 2001 ). PERMANOVA is a distance-based non-parametric MANOVA that allows the analysis of multivariate (or univariate) data in response to treatments in an experimental design. Statistical significant differences between data sets based on metadata (soil parameters, cbbL copy numbers, RubisCO activities) were identified by two-way analysis of variance (ANOVA) and differences were considered significant at P < 0.05. A multiple regression model was built by stepwise regression with significance being defined as P < 0.05. ANOVA and multiple regression analyses were carried out using SPSS (version 16.0, SPSS Inc., USA). The reproducibility of the carried out clone library analysis was tested using the aforementioned replicated clone libraries originating from the rice-rapeseed rotation. The robustness of clone library analysis was assessed based on calculated unweighted UniFrac distances (Lozupone and Knight, 2005 (link)).