Statistical analyses of alpha and beta diversity
Alpha diversity metrics including Shannon index and Chao1 were compared using Kruskal-Wallis tests. For Sorensen-Dice beta diversity, permutational multivariate analysis of variation (PERMANOVA) and Monte-Carlo nonparametric permutation tests were conducted in QIIME to statistically partition the sources of variation in community structure using 999 permutations. Sorensen-Dice dissimilarities among all samples were visualized through ordination using principal coordinates analysis (PCoA) and plots in EMPeror. Pearson correlations and Spearman ranked correlations among log-transformed HSSs and MCSs were conducted with the “stats” package in R v 4.0.4 (R Core Team 2021).