Bacterial diversity
The phyloseq package (McMurdie & Holmes, 2013) was used for downstream analyses of bacterial community data. Amplicon sequence variants (ASVs) were discarded if they were not classified as Bacteria, classified as “Mitochondria”, “Chloroplast”, or were not present in at least two samples. Samples were then rarefied to the sample with the lowest read depth (Hong et al., 2022). Rarefied samples were used to assess beta diversity between site, land cover type, and times of the day. Bray-Curtis distances were visualised in a principal coordinates analysis plot using the ordinate function in phyloseq and permutational multivariate analysis of variance (PERMANOVA) applied with a Type I sum of squares using the adonis function in thevegan package (Oksanen et al., 2013). The effective number of ASVs (alpha diversity) was calculated using the exponent of Shannon’s diversity index values (Jost, 2006). Kruskal-Wallis tests were used to assess the differences in bacterial alpha diversity between sites, land cover types, and times of the day.