Differences between the obtained communities
Redundancy analysis allowed us to measure the amount of variation
explained by differences among habitats and by treatments. Overall,
33%, 24%, and 33% of variability were explained by differences in
habitat for bacteria, fungi, and eukaryotes, respectively. The community
differences among habitats were strongly significant for the three
taxonomic groups (permutation test: all P ≤ 0.001). Differences
among treatments were much weaker, and explained 9%, 2% and 2% of
variation only for bacteria, fungi and eukaryotes, respectively.
Nevertheless, differences were significant for bacteria (permutation
test: P < 0.0001), but not for fungi and eukaryotes
(both P = 1).
For bacteria, contrasts did not detect significant differences between
“control” and treatment 2 or 3. Differences between “control” and
treatment 4 and 5 were significant but explained a limited amount of
variation (for both treatments, ≈3% of variation explained; P< 0.0001; Table 1). We thus used similarity percentage
analysis to identify the MOTUs significantly contributing to these
differences. Only one MOTU showed a significant contribution (P =
0.03 after FDR correction) to the differences between “control” and
treatment 4; this MOTU showed a very limited frequency under treatment 4
(Fig. S1). After FDR correction, no MOTU showed a significant
contribution to the differences between “control” and treatment 5. The
MOTU highlighted by the similarity percentage analysis for treatment 4
also showed a very limited frequency under treatment 5, but these
differences were not significant at the 5% threshold (corrected
significance after FDR correction = 0.078).