Table 2 Enriched and depleted taxa in the differentially abundant OTUs. Enrichment or depletion of taxa at different taxonomic levels within the OTUs that were identified as differentially abundant between plant symbiosis types (see Additional file 1: Table S7) or specifically enriched in symbiotype groups N, A, or AR (see Fig. 3 C & D, Fig. 4, Additional file 1: Table S8). The column “Type” indicates the direction of the relationship and the set of OTUs in which it occurs: The suffix “General” refers to all OTUs that are significant in the indicated contrast, i.e., set union of all OTUs significantly more or less abundant. “Up” refers to OTUs that are significantly more abundant in the first group of the contrast; whereas “Down” refers to OTUs that are significantly less abundant in the first group of the contrast. “Enrichment” indicates that the indicated taxon is significantly more frequent in the set of OTUs tested. “Depletion” indicates that the taxon is significantly less frequent in the set of OTUs tested. Observed and expected values are based on a 2 × 2 contingency table of OTU counts with Fisher’s Exact Test p-values FDR corrected for multiple testing (see Methods, Additional file 1: Fig. S1)
Bacterial OTUs | ||||||
|---|---|---|---|---|---|---|
Contrast or Group | Type | Taxonomic Level | Taxon | Observed | Expected | P-value (FDR) |
Differentially abundant by plant species symbiotic group | ||||||
A vs. N | Depletion Down | Phylum | Firmicutes | 0 | 7.1326 | 0.0078 |
AR vs. N | Depletion General | Acidobacteria | 4 | 18.8632 | 0.0009 | |
AR vs. N | Depletion General | Verrucomicrobia | 3 | 11.3179 | 0.0470 | |
AR vs. N | Depletion General | Chlamydiae | 2 | 9.0779 | 0.0496 | |
AR vs. N | Depletion Down | Acidobacteria | 1 | 12.9871 | 0.0006 | |
AR vs. N | Enrichment Down | Proteobacteria | 187 | 151.7060 | 0.0016 | |
AR vs. N | Depletion Up | Actinobacteria | 8 | 24.0550 | 0.0014 | |
AR vs. A | Depletion General | Chlamydiae | 0 | 7.6009 | 0.0103 | |
AR vs. A | Depletion General | Firmicutes | 11 | 24.8758 | 0.0182 | |
AR vs. A | Depletion General | Acidobacteria | 5 | 15.7942 | 0.0182 | |
AR vs. A | Depletion General | Verrucomicrobia | 2 | 9.4765 | 0.0442 | |
AR vs. A | Enrichment Down | Actinobacteria | 75 | 47.3439 | 0.0015 | |
AR vs. A | Depletion Up | Actinobacteria | 3 | 17.3135 | 0.0002 | |
Symbiotic Group Enriched OTUs | ||||||
Group N | Enrichment | Phylum | Proteobacteria | 52 | 34.9754 | 0.0023 |
Group N | Enrichment | Class | Betaproteobacteria | 24 | 8.1965 | 0.0001 |
Group N | Enrichment | Flavobacteriia | 8 | 0.9357 | 0.0002 | |
Group N | Enrichment | Order | Burkholderiales | 21 | 5.8760 | 0.0000 |
Group N | Enrichment | Flavobacteriales | 8 | 0.9357 | 0.0002 | |
Group N | Enrichment | Family | Flavobacteriaceae | 8 | 0.8421 | 0.0003 |
Group N | Enrichment | Micromonosporaceae | 7 | 0.8234 | 0.0016 | |
Group N | Enrichment | Oxalobacteraceae | 10 | 2.2643 | 0.0044 | |
Group N | Enrichment | Xanthomonadaceae | 7 | 1.4222 | 0.0220 | |
Group AR | Enrichment | Phylum | Proteobacteria | 43 | 24.9200 | 0.0000 |
Group AR | Enrichment | Class | Alphaproteobacteria | 25 | 11.9200 | 0.0048 |
Group AR | Enrichment | Genus | Novosphingobium | 5 | 0.3200 | 0.0086 |
Fungal OTUs | ||||||
None detected | ||||||