Figure 3

Principal component analysis (PCA) with the converted sequence counts of all bacterial groups classified up to the genus level using the centred log-ratio transformation (aldex.clr argument, ALDEx2 package¹⁴) in the unfertilized soil left unamended with permanent beds conventional tilled with residue retained (CT treatment) or permanent beds with crop residue burned (PBB treatment) or permanent beds with crop residue retained (PBC treatment) at day 0, 1 and 3 (filled green square), at day 5, 7 and 14 (filled orange square) and at day 28 and 56 (filled brown square), or ammonium-amended at day 0, 1 and 3 (filled red square), at day 5, 7 and 14 (filled blue square) and at day 28 and 56 (filled black square), and in soil fertilized with 300 kg urea-N ha⁻¹ left unamended at day 0, 1 and 3 (filled green circle), at day 5, 7 and 14 (filled orange circle) and at day 28 and 56 (filled brown circle) or amended with 300 mg NH₄⁺-N kg⁻¹ at day 0, 1 and 3 (filled red circle), at day 5, 7 and 14 (filled blue circle) and at day 28 and 56 (filled black circle) incubated aerobically at 25 ± 2 °C for 56 days. F and p values were determined with a perMANOVA analysis.