Table 2.
Phylogenetic compositions of bacterial isolate collections derived from main roots of sugar beet
| Bacterial isolate collections (%)a | ||||
|---|---|---|---|---|
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| Media | R2A | HM | ||
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| Tissue types | SUb | COb | SU | CO |
| Proteobacteriac | 77.0 | 75.2 | 77.2 | 72.5 |
| Alphaproteobacteria | 48.1 | 52.2 | 46.7 | 64.8* |
| Asticcacaulis | — | — | 1.1 | — |
| Bosea | 5.3 | 5.6 | 6.5 | 11.0 |
| Caulobacter | 2.7 | 0.6 | 4.3 | 3.3 |
| Devosia | 9.1 | 12.4 | 6.5 | 29.7**†† |
| Labrys | 2.1 | 4.3 | — | — |
| Mesorhizobium | 8.0 | 5.0 | 4.3 | 6.6 |
| Rhizobium | 3.2 | 1.2 | 6.5 | 1.1 |
| Sphingomonas | 3.2 | 5.0 | 2.2 | 3.3 |
| Sphingopyxis | 4.3 | 4.3 | 1.1 | — |
| unclassified | ||||
| Bradyrhizobiaceae | 2.7 | 7.5 | — | 3.3 |
| Others | 7.5 | 6.2 | 14.1 | 6.5 |
| Betaproteobacteria | 9.6 | 6.8 | 20.7† | 7.7* |
| Polaromonas | 5.9 | 1.9 | 9.8 | 3.3 |
| Variovorax | 0.5 | 3.1 | 7.6 | 3.3†† |
| Others | 3.2 | 1.8 | 3.3 | 1.1 |
| Gammaproteobacteria | 18.2 | 16.1 | 5.4†† | —*†† |
| Lysobacter | 5.9 | 6.2 | 3.3 | — |
| Pseudoxanthomonas | 9.1 | 6.8 | —†† | 0.0†† |
| Others | 3.2 | 3.1 | 2.1 | — |
| Others | 1.1 | — | 4.3 | — |
| Actinobacteria | 16.6 | 15.5 | 9.8 | 12.1 |
| Aeromicrobium | 3.2 | 3.1 | — | — |
| Marmoricola | 0.5 | — | — | — |
| Microbacterium | 2.1 | 3.1 | 4.3 | 2.2 |
| Mycobacterium | 4.3 | 2.5 | 2.2 | 6.6 |
| Nocardioides | 4.8 | 1.2 | —† | — |
| Others | 1.7 | 5.6 | 3.3 | 3.3 |
| Bacteroidetes | 4.3 | 5.6 | 13.0†† | 15.4†† |
| Dyadobacter | 1.1 | 1.2 | 2.2 | 7.7† |
| Mucilaginibacter | — | — | 4.3†† | 1.1 |
| Pedobacter | 1.6 | 1.9 | 3.3 | 2.2 |
| Others | 1.6 | 2.5 | 3.2 | 4.4 |
| Firmicutes | — | 3.7** | — | — |
| Verrucomicrobia | 2.1 | — | — | — |
a
The relative abundance in a bacterial isolate collection is shown in percentage.
b
SU and CO stand for the surface and core portions of main roots of sugar beet, respectively.
c
Sequences were classified using the Classifier of Ribosomal Database Project II release 10 with a confidence threshold 80%.
*, **
indicate statistical significance examined by the Library Compare of Ribosomal Database Project II at p<0.05 and p<0.01, respectively, between SU and CO in each medium.
†, ††
indicate statistical significance examined by the Library Compare of Ribosomal Database Project II at p<0.05 and p<0.01, respectively, between R2A and HM in each of SU and CO.