Table 4.
Phyllogenetic compositions of major taxa for root- and tuber-assoicated bacteria in 8 potato genotypes.
| Phyllogenetic compositiona | Clone libraries (%) | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Root | Tuber | |||||||||||||||
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| R1b | R2 | R3 | M1 | M2 | S1 | S2 | S3 | R1 | R2 | R3 | M1 | M2 | S1 | S2 | S3 | |
| Actinobacteria | 11.5 | 9.1 | 8.7 | 3.7** | 11.8 | 8.6 | 6.1 | 9.6 | 3.0 | 3.8 | 2.3 | 10.3 | 8.7 | 15.2** | 13.6** | 23.2** |
| Rhodococcus | 1.9 | 3.0 | 2.9 | — | 3.5 | 4.0 | 1.2 | 1.7 | 1.5 | 1.9 | — | — | 1.4 | 12.0** | 8.6* | 20.0** |
| Streptomyces | 3.8 | 1.2 | 2.3 | —* | 4.1 | 0.6* | 1.2 | 1.1 | — | — | 2.3 | — | 1.4 | 1.1 | 1.2 | — |
| Arthrobacter | 1.9 | 3.0 | 1.7 | 1.9 | 2.4 | 1.7 | 1.8 | 1.7 | 0.7 | — | — | 1.0 | — | 1.1 | 1.2 | 2.1 |
| Bacteroidetes | — | — | — | — | 1.8 | — | — | — | — | — | — | — | — | — | — | — |
| Flavobacterium | — | — | — | — | 1.8 | — | — | — | — | — | — | — | — | — | — | — |
| Chloroflexi | 0.6 | — | — | 0.6 | — | 0.6 | — | — | — | — | — | — | — | — | — | — |
| Firmicutes | 21.8 | 18.2 | 12.7* | 19.8 | 13.5 | 10.3** | 18.9 | 15.8 | 38.5 | 35.8 | 69.8** | 59.8** | 50.7 | 26.1 | 9.9** | 41.1 |
| Clostridia | — | — | — | 0.6 | 0.6 | — | — | — | 0.7 | — | 7.0 | 4.1 | 1.4 | 1.1 | — | — |
| Bacilli | 21.8 | 18.2 | 12.7* | 19.2 | 12.9* | 10.3** | 18.9 | 15.8 | 36.3 | 35.8 | 60.5** | 54.6** | 49.3 | 25.0 | 8.6** | 37.9 |
| Paenibacillus | 18.6 | 12.1 | 8.1** | 16.7 | 12.9 | 8.6** | 12.2 | 10.2* | 3.0 | 3.8 | — | 3.1 | 13.0** | 4.3 | — | 3.2 |
| Bacillus | 2.6 | 5.5 | 4.6 | 2.5 | — | 1.7 | 5.5 | 5.1 | 32.6 | 30.2 | 58.1** | 40.2 | 29.0 | 18.5* | 8.6** | 32.6 |
| Gemmatimonadetes | — | — | — | — | — | 0.6 | — | — | — | — | — | — | — | — | — | — |
| Planctomycetes | 5.1 | 2.4 | 3.5 | 2.5 | 4.7 | 9.7 | 4.9 | 1.7 | — | — | — | 1.0 | — | 3.3 | 2.5 | — |
| Zavarzinella | 1.9 | 0.6 | 0.6 | 0.6 | 0.6 | 1.7 | 0.6 | 0.6 | — | — | — | — | — | 2.2 | 2.5 | — |
| Proteobacteria | 57.7 | 67.3 | 72.8** | 73.5** | 64.7 | 62.9 | 64.0 | 68.4 | 57.8 | 60.4 | 23.3** | 27.8** | 40.6* | 51.1 | 74.1* | 35.8** |
| Alphaproteobacteria | 13.5 | 21.2 | 26.6** | 27.2** | 28.2** | 36.6** | 18.9 | 32.8** | 49.6 | 45.3 | 18.6** | 19.6** | 31.9* | 43.5 | 65.4* | 18.9** |
| Phyllobacterium | — | 2.4 | — | — | — | — | 0.6 | — | 44.4 | 13.2** | 7.0** | 7.2** | 7.2** | 30.4* | 48.1 | 1.1** |
| Rhizobium | 2.6 | 6.7 | 13.3** | 14.8** | 8.2* | 21.1** | 7.9* | 16.4** | 2.2 | 1.9 | 4.7 | — | 4.3 | 8.7* | 9.9* | 5.3 |
| Devosia | 1.9 | 1.2 | 1.7 | 1.9 | 2.4 | 1.1 | 1.2 | 2.3 | — | — | — | — | 1.4 | — | 1.2 | — |
| Betaproteobacteria | 3.2 | 10.3* | 3.5 | 7.4 | 5.9 | 5.7 | 8.5 | 5.6 | 1.5 | 5.7 | — | 1.0 | — | 4.3 | 4.9 | 1.1 |
| Gammaproteobacteria | 33.3 | 35.2 | 37.0 | 37.0 | 28.2 | 19.4** | 27.4 | 24.3 | 5.9 | 7.6 | 4.7 | 6.2 | 7.2 | 3.3 | 2.5 | 15.8* |
| Aquicella | 18.6 | 15.8 | 9.2* | 13.0 | 7.1** | 9.1* | 7.9** | 6.8** | — | 1.9 | — | 3.1 | — | 1.1 | — | — |
| Pseudomonas | — | 2.4 | 3.5* | 2.5 | 1.2 | 1.1 | 1.2 | 2.8* | 0.7 | 5.7* | 4.7 | — | 4.3 | — | 1.2 | 4.2 |
| Unclassified | ||||||||||||||||
| Gammaproteobacteria | 12.8 | 9.7 | 16.8 | 9.3 | 4.1 | 5.1 | 11.0 | 5.1 | — | — | — | 1.0 | 1.4 | 1.1 | 1.2 | 1.1 |
| Deltaproteobacteria | 6.4 | 0.6** | 5.8 | 1.2* | 1.2* | 1.1* | 7.3 | 5.6 | — | 1.9 | — | 1.0 | — | — | — | — |
| Verrucomicrobia | 1.3 | 1.8 | 1.2 | 0.0 | 3.5 | 5.7* | 3.7 | 4.0 | — | — | — | — | — | 2.2 | — | — |
| Bacteria_incertae_sedis | — | — | — | 0.6 | 1.8 | 0.6 | — | — | — | — | — | — | — | — | — | — |
| Unclassified Bacteria | 1.9 | 1.2 | 1.2 | — | — | 1.7 | 2.4 | 0.6 | 0.7 | — | 4.7 | 1.0 | — | 2.2 | — | — |
Sequences were grouped using the RDP Classifier of the Ribosomal Database Project-II release 11 with a confidence threshold of 80%.
R, M, and S indicate the phenotypes of the 8 potato genotypes; resistant, medium resistant, and susceptible to potato scab diseases, respectively. R1, R2, R3, M1, M2, S1, S2, and S3 are designated for clone libraries of the 8 potato genotypes (Yukirasha, 02005-10, Snow March, Star Ruby, Snowden, Irish Cobbler, Toyoshiro, and Piruka, respectively). CD stands for the isolate collections derived from roots or tubers of cultivar “Yukirasha”.
indicate significance at the 5% and 1% levels (P<0.05 and P<0.01), respectively, calculated with the Library Compare of RDP II, between R1 and other libraries.