TABLE 2.
Diversity of cultivated bacteria extracted from rhizospheres of M. sativa and C. album plants collected from S. meliloti L33-inoculated and noninoculated field plots and characterized by using ARDRA and the nucleotide sequence of PCR-amplified 16S rRNA genes
| ARDRA groupa | No. of isolatesb
|
Phylogenetic assignmentc | Closest relative | % Similarity to closest relative | Representative strain (GenBank accession no.) | ||||
|---|---|---|---|---|---|---|---|---|---|
| Total | M. sativa, inoculated | M. sativa, noninoculated | C. album, inoculated | C. album, noninoculated | |||||
| AA | 25 | 2 | 1 | 9 | 13 | α-Proteobacteria | Agrobacterium rubi | 99.5 | FSC127 (AF214119) |
| AB | 19 | 9 | 0 | 5 | 5 | α-Proteobacteria | Phyllobacterium myrsinacearum | 98.0 | FSC650 (AF214120) |
| B | 9 | 6 | 0 | 2 | 1 | α-Proteobacteria | Phyllobacterium rubiacearum | 98.9 | FSC635 (AF214121) |
| CA | 9 | 5 | 1 | 1 | 2 | α-Proteobacteria | Rhizobium leguminosarum | 99.5 | FSC115 (AF214122) |
| CB | 25 | 10 | 0 | 9 | 6 | α-Proteobacteria | Rhizobium sp. (partial) strain 21321 | 99.1 | FSC117 (AF214123) |
| CC | 17 | 6 | 0 | 9 | 2 | α-Proteobacteria | Rhizobium sp. strain USDA 1920 | 100 | FSC177 (AF214124) |
| CD | 25 | 25 | 0 | 0 | 0 | α-Proteobacteria | Sinorhizobium meliloti | 100 | FSC302 (AF214125) |
| CE | 4 | 2 | 1 | 1 | 0 | α-Proteobacteria | Ensifer adhaerens | 99.3 | FSC375 (AF214126) |
| DA | 212 | 25 | 13 | 85 | 89 | β-Proteobacteria | Variovorax sp. strain WFF052 | 99.3 | FSC781 (AF214127) |
| DB | 46 | 8 | 5 | 17 | 16 | β-Proteobacteria | Variovorax paradoxus | 99.1 | FSC933 (AF214128) |
| DC | 14 | 0 | 1 | 8 | 5 | β-Proteobacteria | Variovorax paradoxus | 99.6 | FSC917 (AF214129) |
| EA | 5 | 0 | 0 | 1 | 4 | β-Proteobacteria | Burkholderia sp. isolate N3P2 | 98.1 | FSC1134 (AF214130) |
| EB | 16 | 2 | 2 | 7 | 5 | β-Proteobacteria | Burkholderia glathei | 99.9 | FSC1120 (AF214131) |
| EC | 15 | 2 | 0 | 10 | 3 | β-Proteobacteria | Burkholderia sp. strain LB400 | 99.0 | FSC1145 (AF214132) |
| ED | 7 | 0 | 0 | 5 | 2 | γ-Proteobacteria | Erwinia amylovora | 98.9 | FSC1186 (AF214133) |
| FA | 61 | 9 | 32 | 1 | 19 | γ-Proteobacteria | Pseudomonas sp. strain IC038 | 99.0 | FSC408 (AF214134) |
| FB | 50 | 6 | 31 | 3 | 10 | γ-Proteobacteria | Pseudomonas putida | 99.3 | FSC413 (AF214135) |
| FC | 11 | 0 | 8 | 0 | 3 | γ-Proteobacteria | Pseudomonas sp. strain S2 | 100 | FSC410 (AF214136) |
| FD | 6 | 4 | 2 | 0 | 0 | γ-Proteobacteria | Pseudomonas sp. strain PsF | 99.2 | FSC472 (AF214137) |
| G | 109 | 8 | 101 | 0 | 0 | γ-Proteobacteria | Acinetobacter calcoaceticus | 100 | FSC001 (AF214138) |
| H | 9 | 7 | 0 | 1 | 1 | γ-Proteobacteria | Stenotrophomonas maltophilia | 99.8 | FSC630 (AF214139) |
| IA | 17 | 4 | 1 | 10 | 2 | F-C group | Flavobacterium johnsonae | 97.4 | FSC841 (AF214140) |
| IB | 15 | 7 | 0 | 6 | 2 | F-C group | Flexibacter columnaris | 98.1 | FSC231 (AF214141) |
| JA | 124 | 63 | 35 | 18 | 8 | GP bacteria | Arthrobacter ramosus | 99.7 | FSC1047 (AF214142) |
| JB | 9 | 7 | 1 | 0 | 1 | GP bacteria | Arthrobacter oxidans | 99.2 | FSC285 (AF214143) |
| Total | 859 | 217 | 235 | 208 | 199 | ||||
The on-line letter indicates the group based on fragment length polymorphism obtained after digestion of the PCR-amplified 16S rRNA gene product with HhaI. The subscript letter indicates the subgroup based on results obtained with restriction endonuclease HaeIII.
The Pearson correlation coefficient for inoculated and noninoculated M. sativa was 0.270. The Pearson correlation coefficient for inoculated and noninoculated C. album was 0.949.
α-Proteobacteria, α subgroup of the Proteobacteria; β-Proteobacteria, β subgroup of the Proteobacteria; γ-Proteobacteria, γ subgroup of the Proteobacteria; F-C group, Flavobacterium-Cytophaga group; GP bacteria, gram-positive bacteria with high G+C DNA contents.