Bacterial networks
The association network analyses highlighted differences in community complexity and interactions across sampling times and land cover types, defined by node degree (the average number of edges connecting the vertices), network size, and edge weight (i.e., whether the interactions were positive or negative) (Figure 4). At the phylum level, bacterial ASVs in the cleared plots had a higher node degree (total x̅ node degree = 45.2) than the native plots (total x̅ node degree = 36) (t = -3.18, df = 148, p = <0.01).
There were also clear differences in the node degree across sampling times. The Mark Oliphant CP cleared plot had a steadily increasing node degree from 00:00 through to 18:00. Moreover, the mean node degree was typically higher for native plots between 00:00 and 06:00 (combined x̅ node degree =19.9) than between 12:00 and 18:00 (combined x̅ node degree =16.1) (t = 2.22, df = 80, p = 0.02) but was generally lower for cleared plots between 00:00 and 06:00 (combined x̅ node degree =18.4) than between 12:00 and 18:00 (combined x̅ node degree =26.8) (t = -4.36, df = 83, p = <0.01).
Evaluation of either positive or negative edge types highlighted differences across land cover types with more negative associations among ASVs in the native plots. One striking finding was that the mean edge weight between 00:00 and 06:00 in the native Mark Oliphant CP plot dropped from 0.88 (a high level of positive interactions) to 0.10 (a high level of negative interactions).
At the genus level (Figure 5), bacterial ASVs in the cleared plots had a higher node degree (total x̅ node degree = 27.6) than the native plots (total x̅ node degree = 20.3), as expected following the phylum-level analysis. There were also clear differences in the node degree across sampling times; however, the patterns were variable. The native Kenneth Stirling CP plot had a steadily decreasing node degree from 00:00 through to 18:00. The cleared Kenneth Stirling CP plot had a steadily increasing node degree from 18:00 to 12:00. There were also differences in edge weights across site types with more negative associations among ASVs in the native sites (combined x̅ edge weight = 4.78) than cleared plots (combined x̅ edge weight = 5.47). The striking difference in mean edge weight between 00:00 and 06:00 in the native Mark Oliphant CP plot was also visible in the genus-level network plots. Conversely, the mean edge weight increased between native Kenneth Stirling CP plot at 00:00 and 06:00.
The evaluation of hub taxa (bacterial groups with the highest degree of either positive or negative associations) showed that the keystone bacteria at the genus level were different at each sampling time for both the native and cleared plots, with positive degree ranging from 4 to 19 and negative degree ranging from 0 to 15 (Table 2). At the phylum level, Acidobacteriota were the most common taxa with the highest number of positive associations, occurring in native Kenneth Stirling and Mark Oliphant CP plots at 18:00 and the cleared Mark Oliphant CP plot at 06:00 and 12:00. Bdellovibrionota were the top negative hub taxa, featuring in native Kenneth Stirling CP 00:00, native Mark Oliphant CP 12:00, and cleared Mark Oliphant CP 12:00.