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).