Figure 2

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 or soil fertilized with 300 kg urea-N ha⁻¹ left unamended with conventional tilled beds (CT) 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), permanent beds with crop residue burned (PBB) 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) and permanent beds with crop residue retained (PBC) at day 0, 1 and 3 (filled green triangle), at day 5, 7 and 14 (filled orange triangle) and at day 28 and 56 (filled brown triangle) or amended with 300 mg NH₄⁺-N kg⁻¹ dry soil with CT 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), PBB 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) and PBC at day 0, 1 and 3 (filled red triangle), at day 5, 7 and 14 (filled blue triangle) and at day 28 and 56 (filled black triangle), incubated aerobically at 25 ± 2 °C for 56 days. F and p values were determined with a perMANOVA analysis.