Permutational multivariate analysis of variance.

Permutational multivariate analysis of variance was used to test the effect of the interaction between site and management on microbial community composition (adonis function of vegan package), separately for bacteria and fungi. If the interaction was significant, the magnitude of the management effect was then tested within each site. If the interaction was not significant, permutational multivariate analysis of variance (PERMANOVA) was used to test the relative magnitude of site and management effects. Redundancy analysis (RDA) was conducted to identify soil physicochemical properties with the greatest influence on rhizosphere microbial community composition. Parameters that significantly explained variation in bacterial or fungal community composition were identified using forward selection (ordistep function of vegan package).