TABLE 3.
Mean contribution of the major T-RFs found in the soybean nodule surface samples, in each of the six data sets, for both inoculated treatments sampled at both time points
| RE | Major T-RF length (nt) | % Hup+ (n = 3) | % Hup− (n = 3) | Fold difference between Hup− and Hup+ | Phylogenetic affiliation (putative genus)a |
|---|---|---|---|---|---|
| BstUI | 93 | 7.7 | 14.1 | 1.8 | Mesorhizobium/Rhizobium |
| 95 | 9.4 | 15.1 | 1.6 | Sphingopyxis | |
| 97 | 6.2 | 11.8 | 1.9 | Bradyrhizobium | |
| 220 | 2.4 | 10.9 | 4.5 | Mycobacterium | |
| 223 | 6.6 | 6.8 | 1.0 | Kribbella | |
| HaeIII | 65 | 3.6 | 10.5 | 2.9 | Mycobacterium |
| 189 | 5.8 | 9.4 | 1.6 | Rhizobium | |
| 194 | 16.2 | 17.9 | 1.1 | Bradyrhizobium | |
| 224 | 13.9 | 11.6 | 0.8 | Mesorhizobium | |
| 226 | 23.0 | 10.5 | 0.5 | Paenibacillus | |
| 292 | 12.2 | 17.3 | 1.4 | Sphingopyxis | |
| HhaI | 59 | 2.9 | 5.4 | 1.9 | Mesorhizobium |
| 80 | 5.8 | 7.0 | 1.2 | Sphingopyxis | |
| 206 | 12.4 | 17.1 | 1.4 | ND | |
| 338 | 3.4 | 6.3 | 1.9 | Rhizobium | |
| 365 | 2.8 | 20.8 | 7.4 | Mycobacterium | |
| 472 | 14.9 | 22.1 | 1.5 | Bradyrhizobium | |
| HinfI | 99 | 2.6 | 3.3 | 1.3 | Mesorhizobium |
| 101 | 4.2 | 6.5 | 1.5 | Sphingopyxis | |
| 166 | 1.0 | 7.0 | 7.0 | Mycobacterium | |
| 321 | 7.3 | 6.8 | 0.9 | ND | |
| 472 | 13.4 | 10.9 | 0.8 | Bradyrhizobium | |
| MspI | 126 | 1.4 | 4.8 | 3.4 | Mesorhizobium/Rhizobium |
| 151 | 4.1 | 11.3 | 2.8 | Bradyrhizobium | |
| 160 | 2.9 | 3.5 | 1.2 | ND | |
| 170 | 0.3 | 9.5 | 31.7 | Mycobacterium | |
| 399 | 2.9 | 11.7 | 4.0 | ND | |
| Sau96I | 64 | 2.0 | 9.0 | 4.5 | Mycobacterium |
| 164 | 4.2 | 8.3 | 2.0 | Sphingopyxis | |
| 189 | 27.7 | 14.8 | 0.5 | Rhizobium | |
| 192 | 9.8 | 13.2 | 1.3 | Bradyrhizobium | |
| 289 | 8.2 | 9.1 | 1.1 | Mesorhizobium | |
| 291 | 3.4 | 5.6 | 1.6 | ND | |
| 317 | 5.6 | 2.7 | 0.5 | ND |
a
Phylogenetic affiliation by genus is given if it was able to be determined from the sequences in the parallel clone library. “ND” indicates that a phylogenetic affiliation was not able to be determined from the predicted T-RFs within 1 nt of the clone library sequences obtained.