Fig. 4

Differential abundance analysis. A. Differentially abundant microbial phylum identified by ANCOM. Volcano plot of differential abundance at the group level (topsoil and subsoil), clr are represented on the x-axis and W-statistics on the y-axis. The crl (center log ratio) is a measure of the effect size difference for a particular species between the study groups, and the W-statistic represents the number of times of the null-hypothesis (the average abundance of a given phylum in a group is equal to that in the other group) was rejected for a given phylum. p-values with good control of the Benjamini-Hochberg correction (FDR) at 5% type I error rate, are already embedded in the ANCOM test before the final significance based on the empirical distribution of a count random variable called W. B. Box plot comparing relative abundances between topsoil samples (violet) and subsoil samples (orange) of the phyla identified as differentially abundant. The bottom and top of a box are the 25th and 75th quartiles, the horizontal line within a box is the median, and the ends of the whiskers are the limits of the distribution as inferred from the upper and lower quartiles. Dots are samples. Note that significance of phyla among groups was tested using three approaches. First we performed an ANCOM test, followed by a metagenomeSeq analysis and after a more conservative univariate analysis using Mann-Whitney U test (p < 0.05). *Asterisk the phyla that were considered enriched were those that were significantly enriched in at least two of the three (Additional file 6: Table S6)