FIG 3.

LDA effect size cladograms comparing the total resident (DNA-based) and metabolically active (RNA-based) prokaryotic community profiles. Separate analyses were performed on bulk soil, maize rhizosphere, and maize endosphere. Circles represent phylogenetic levels from kingdom to family from the center outwards. The colored nodes and shading denote significant differences in relative abundance between specific taxa in the conventional (red) or diversified (green) system; yellow node, no significant difference. 1, Alphaproteobacteria (1a, Sphingomonadaceae and Erythrobacteraceae; 1b, Burkholderiales; 1c, Rhizobiaceae; 1d, Bradyrhizobiaceae); 2, Betaproteobacteria; 3, Pseudomonadales; 4, Thaumarchaeota; 5, Actinobacteria; 6, Rubrobacteria; 7, Bacteroidetes; 8, Cyanobacteria; 9, Nitrospiraceae; 10, Nitrosomonadaceae; 11, Deltaproteobacteria; 12, Euryarchaeota; 13, Acidobacteria; 14, Elusimicrobia; 15, Planctomycetes; 16, Spirochaetae; 17, Verrucomicrobia; 18, Flavobacteria; 19, Ktedonobacteria; 20, Holophagae; 21, Chloroflexi.