Hypothesis testing framework and consensus approach to verify differences in α and β microbial diversity.

ANOVAs (on ASVs frequencies) and PERMANOVAs (on either ASVs frequencies or centered log-ratio transformed, compositional data, CLR-CoDa) were used to test univariate and multivariate location effects of management practice (Ma: conventional vs agroecological), altitude (Al: high vs low), crop (Cr: watermelon vs cucumber), and site (list and coordinates in S1 File). PERMDISP, based on CLR-CoDa, was used to test dispersion effects on β diversity (Anna Karenina principle) promoted by different management practices either at high or low altitudes. FDR: p value corrected via False Discovery Rate. Tests on α microbial diversity considered Abundance Coverage Estimator (ACE), Faith’s Phylogenetic Diversity (PD), Shannon-Weiner (H) and the Inverse Simpson indexes (IS). The results of the posthoc tests implemented for Ma x Al are indicated. *: P = <0.05; **: P = <0.001; ***: P = <0.0001. For detailed results see sheets "ANOVA", PERMANOVA", "PERMDISP".
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