Table 1.
Functional distribution of the Bradyrhizobium and Burkholderia differentially expressed (DE) KOs between rhizosphere and rhizoplane samples
| Bradyrhizobium | Burkholderia | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Individual functional categories | Background | Rhizoplane downregulated | p value | Rhizoplane upregulated | p value | Background | Rhizoplane downregulated | p value | Rhizoplane upregulated | p value |
| Metabolism of cofactors and vitamins | 105 | 6 | 0.84 | 8 | 0.86 | 143 | 1 | 0.04 | 5 | 1 |
| Metabolism of other amino acids | 51 | 5 | 0.40 | 4 | 1 | 55 | 4 | 0.28 | ||
| Metabolism|unclassified | 121 | 9 | 0.71 | 18 | 0.04 | 148 | 4 | 0.66 | 3 | 0.49 |
| Metabolism of terpenoids and polyketides | 40 | 2 | 1 | 3 | 1 | 76 | 1 | 0.37 | 2 | 1 |
| Energy metabolism | 149 | 31 | 5.6E−8 | 9 | 0.29 | 146 | 17 | 6.6E−5 | 3 | 0.48 |
| Enzyme families | 81 | 3 | 0.36 | 7 | 1 | 88 | 3 | 1 | 2 | 0.77 |
| Amino acid metabolism | 223 | 15 | 1 | 15 | 0.31 | 272 | 35 | 1.4E−10 | 6 | 0.29 |
| Xenobiotics biodegradation and metabolism | 97 | 6 | 1 | 10 | 0.59 | 108 | 10 | 0.01 | 2 | 0.59 |
| Biosynthesis of other secondary metabolites | 19 | 1 | 1 | 3 | 0.42 | 23 | 3 | 0.07 | ||
| Nucleotide metabolism | 73 | 7 | 0.35 | 9 | 0.31 | 92 | 2 | 0.58 | 5 | 0.38 |
| Carbohydrate metabolism | 195 | 21 | 0.04 | 10 | 0.08 | 237 | 17 | 0.01 | 3 | 0.06 |
| Lipid metabolism | 71 | 4 | 1 | 5 | 0.83 | 86 | 5 | 0.39 | 3 | 1 |
| Glycan biosynthesis and metabolism | 41 | 5 | 0.42 | 63 | 1 | 0.73 | 1 | 0.72 | ||
| Membrane transport | 180 | 7 | 0.15 | 18 | 0.58 | 307 | 13 | 0.75 | 15 | 0.19 |
| Signaling molecules and interaction | 3 | 1 | 0.29 | |||||||
| Genetic information processing | 40 | 7 | 0.03 | 1 | 0.25 | 69 | 1 | 0.52 | 1 | 0.52 |
| Folding, sorting, and degradation | 51 | 10 | 0.004 | 3 | 0.62 | 75 | 3 | 0.76 | 4 | 0.35 |
| Replication and repair | 89 | 8 | 0.40 | 8 | 1 | 115 | 1 | 0.13 | 6 | 0.31 |
| Translation | 101 | 4 | 0.41 | 11 | 0.48 | 138 | 2 | 0.17 | 3 | 0.48 |
| Signal transduction | 121 | 3 | 0.08 | 17 | 0.002 | 120 | 4 | 1 | 9 | 0.04 |
| Transcription | 81 | 5 | 1 | 118 | 3 | 0.62 | 5 | 0.61 | ||
| Cellular processes and Ssignaling | 128 | 11 | 0.47 | 14 | 0.42 | 204 | 2 | 0.03 | 11 | 0.17 |
| Cell growth and death | 14 | 1 | 1 | 8 | 1 | 0.27 | ||||
| Transport and catabolism | 9 | 1 | 0.57 | |||||||
| Cell motility | 50 | 7 | 0.002 | |||||||
Background, the functional distribution of Bradyrhizobium or Burkholderia KOs in all the samples. The KEGG level 2 pathway was used for the functional classification. Rhizoplane-downregulated, the DE KOs show higher expression level in rhizosphere samples than in rhizoplane samples. Rhizoplane-upregulated, the DE KOs show higher expression level in rhizoplane samples than in rhizosphere samples. p value, Fisher’s exact test, two-tail. The significant p values were italicized, and the underrepresented items were bolded