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.