Bacterial Community and Diversity
After cleaning and filtering of sequence data, a total of 12,173
bacterial amplicon sequence variants (ASVs) were detected across the 96
samples (Table S1). Sample reads were rarefied to the lowest read count
of 23,073 reads (from #30 sample – KSN 00:00 week 6; Table S1). The
effective number of ASVs was calculated to compare alpha diversity
between sites, land cover, and times. Alpha diversity at Mark Oliphant
CP was higher than Kenneth Stirling CP (mean ± SD, Mark Oliphant CP: 554
± 132 effective number of ASVs; Kenneth Stirling CP: 479 ± 149 effective
number of ASVs; chi-squared = 6.28, p = 0.012; Figure 2a). Alpha
diversity was higher at the cleared land cover type at Kenneth Stirling
CP (cleared: 519 ± 123 effective number of ASVs; native: 439 ± 164
effective number of ASVs; chi-squared = 4.42, p = 0.035) and at
Mark Oliphant CP (cleared: 603 ± 104 effective number of ASVs; native:
504 ± 139 effective number of ASVs; chi-squared = 8.82, p =
0.003; Figure 2a).
Time did not have an effect on alpha diversity in Kenneth Stirling CP at
either the cleared (mean ± SD; 00:00: 505 ± 109 effective number of
ASVs; 06:00: 513 ± 132 effective number of ASVs; 12:00: 529 ± 161
effective number of ASVs; 18:00: 529 ± 119 effective number of ASVs;
chi-squared = 0.313, p = 0.957; Figure 2b) or native land cover
plot (00:00: 520 ± 140 effective number of ASVs; 06:00: 339 ± 180
effective number of ASVs; 12:00: 462 ± 203 effective number of ASVs;
18:00: 436 ± 99.4 effective number of ASVs; chi-squared = 4.547,p = 0.208; Figure 2b). Time also had no effect on alpha diversity
at Mark Oliphant CP at the cleared (00:00: 602 ± 134 effective number of
ASVs; 06:00: 589 ± 88.3 effective number of ASVs; 12:00: 591 ± 82
effective number of ASVs; 18:00: 631 ± 127 effective number of ASVs;
chi-squared = 0.393, p = 0.942; Figure 2c) or native land cover
type (00:00: 591 ± 188 effective number of ASVs; 06:00: 518 ± 103
effective number of ASVs; 12:00: 450 ± 105 effective number of ASVs;
18:00: 457 ± 129 effective number of ASVs; chi-squared = 2.61, p= 0.456; Figure 2c).
The principal coordinate analysis and PERMANOVA based on Bray-Curtis
distance showed that land cover (p = 0.001) had a stronger and
significant effect on beta diversity than site (p = 0.001) and
time (p = 1.0) (Figure 2d). The site effect was stronger in the
cleared land cover types, with Kenneth Stirling CP and Mark Oliphant CP
samples separating more distinctly than in the native land cover (Figure
2d). There was also a greater bacterial community heterogeneity measured
by distance to the centroid in the native land cover plot compared to
the cleared land cover plot in Kenneth Stirling CP (mean ± SD; cleared:
0.477 ± 0.062 distance to centroid; native: 0.534 ± 0.0456 distance to
centroid; P-adj = 0.001, 95% CI [-0.096, -0.018]; Figure 3). The
same trend was seen in land cover at Mark Oliphant CP though this was
not significant (cleared: 0.483 ± 0.046; native: 0.508 ± 0.040; P-adj =
0.351, 95% CI [-0.063, - 0.014]; Figure 3).