Table 2.
Phylogenetic compositions of 16S rRNA gene libraries and isolate collections derived from potato tissues
| Phylogenetic compositions (%)a | Clone libraries | Isolate collections | ||||||
|---|---|---|---|---|---|---|---|---|
|
|
|
|||||||
| Leaf | Stem | Root | Tuber | Leaf | Stem | Root | Tuber | |
| Proteobacteria | 84.0 | 89.7 | 65.7 | 62.0 | 62.4 | 57.7 | 72.9 | 60.4 |
| Alphaproteobacteria | 40.7 | 43.7 | 32.5 | 50.0 | 62.4 | 53.7 | 38.2 | 42.5 |
| Methylobacterium | 9.3 | 7.5 | — | 1.9 | 41.0 | 35.4 | — | — |
| Rhizobium/Agrobacterium | 18.7 | 29.9 | 8.9 | 18.0 | 2.4 | — | 6.0 | 8.5 |
| Mesorhizobium | — | — | 4.7 | 3.7 | — | — | 5.5 | 3.3 |
| Phyllobacterium | — | — | 3.0 | 14.3 | — | — | 1.5 | 1.4 |
| Caulobacter | — | — | — | — | — | — | 8.5 | 14.6 |
| Devosia | 0.7 | — | 3.6 | — | — | — | 2.0 | 0.9 |
| Sphingomonas | 8.0 | 3.4 | 1.8 | 8.1 | 19.0 | 17.7 | 8.0 | 2.4 |
| Other genera | 4.0 | 2.9 | 8.1 | 3.4 | — | 0.6 | 4.2 | 4.8 |
| Unclassified | ||||||||
| Alphaproteobacteria | — | — | 2.4 | 0.6 | — | — | 2.5 | 6.6 |
| Betaproteobacteria | 3.3 | — | 5.9 | 5 | — | 4.0 | 31.7 | 17.5 |
| Polaromonas | — | — | — | 3.7 | — | — | 8.5 | 8.5 |
| Variovorax | — | — | — | — | 2.3 | 3.5 | 0.5 | |
| Pelomonas | — | — | — | — | — | — | 2.5 | 4.7 |
| Methylibium | — | — | — | — | — | — | 4.5 | — |
| Other genera | 3.3 | — | 5.9 | 1.3 | — | 1.7 | 12.7 | 3.8 |
| Gammaproteobacteria | 40.0 | 46.0 | 26.6 | 5.0 | — | — | 3.0 | 0.5 |
| Acinetobacter | — | 36.2 | — | — | — | — | — | — |
| Pseudomonas | 10.0 | 0.6 | 0.6 | 2.5 | — | — | — | — |
| Erwinia | 4.7 | 1.1 | — | — | — | — | — | — |
| Pantoea | 6.0 | 2.9 | — | — | — | — | — | — |
| Other genera | 3.3 | 1.8 | 5.2 | 1.9 | — | — | 3.0 | 0.5 |
| Unclassified | ||||||||
| Enterobacteriaceae | 16.0 | 3.4 | — | — | — | — | — | — |
| Unclassified | ||||||||
| Chromatiales | — | — | 3.6 | — | — | — | — | — |
| Unclassified | ||||||||
| Gammaproteobacteria | — | — | 17.2 | 0.6 | — | — | — | — |
| Deltaproteobacteria | — | — | 0.6 | — | — | — | — | — |
| Actinobacteria | 9.3 | 10.3 | 10.7 | 5 | 37.6 | 39.4 | 14.6 | 17.0 |
| Microbacterium | — | 1.1 | — | — | 36.1 | 37.7 | — | 1.4 |
| Arthrobacter | 6.7 | 8.0 | 1.2 | — | — | 0.6 | 0.5 | — |
| Streptomyces | — | — | 4.1 | 1.2 | — | — | 6.5 | 2.8 |
| Other genera | 2.6 | 1.2 | 5.4 | 3.8 | 1.5 | 1.1 | 7.6 | 12.8 |
| Firmicutes | 6.7 | — | 10.1 | 32.0 | — | 0.6 | 0.5 | 0.5 |
| Paenibacillus | — | — | 7.1 | 5.0 | — | — | — | — |
| Bacillus | 1.3 | — | 3.0 | 25.0 | — | 0.6 | — | 0.5 |
| Other genera | 5.4 | — | — | 2.0 | — | — | 0.5 | — |
| Bacteroidetes | — | — | 2.4 | — | — | 2.3 | 12.1 | 21.7 |
| Pedobacter | — | — | — | — | — | 2.3 | 1.0 | 12.3 |
| Chitinophaga | — | — | 0.6 | — | — | — | 3.5 | 0.5 |
| Lacibacter | — | — | — | — | — | — | — | 4.2 |
| Other genera | — | — | 1.8 | — | — | — | 7.6 | 4.7 |
| Planctomycetes | — | — | 8.9 | — | — | — | — | — |
| Schlesneria | — | — | 4.1 | — | — | — | — | — |
| Other genera | — | — | 4.8 | — | — | — | — | — |
| Verrucomicrobia | — | — | 1.2 | — | — | — | — | — |
| Acidobacteria | — | — | 0.6 | — | — | — | — | — |
| Bacteria_incertae_sedis | — | — | 0.6 | — | — | — | — | — |
| Unclassified Bacteria | — | — | — | 1.9 | — | — | — | 0.5 |
a
16S rRNA gene sequences were classified by RDP Classifier. The compositions of genera are shown for only dominant groups.