Fig. 3

Cave microbial communities are richer, harbour more abundant bacterial taxa and are phylogenetically distinct from surface communities. ASV richness (A) and core dominance (proportion of ASVs with > 0.2% relative abundance across > 50% of the samples) (B) across cave zones. Post-hoc results based on pair-wise comparisons between soil zones are indicated with letters. C NMDS plot showing bacterial community similarities (Bray–Curtis distances) among sampling zones and caves (stress = 0.0701). Colours of sampling zones are the same as the colours in panels A and B. Arrows indicate the four environmental variables that were significantly associated with the observed differences in bacterial community compositions. Ellipses represent the 95% confidence intervals. D Relative abundance of major bacterial phyla and the 20 most abundant bacterial orders (E) across sampling zones