Table 2.
Identification and comparison of rhizobacterial species of Rahnella and Serratia in MGMRh and MGNRh by shotgun metagenomic approaches.
| Bioinformatics Tool | SOAPaligner | One Codex Data Platform | ||||
|---|---|---|---|---|---|---|
| Database | NCBI nucleotide database | One Codex DB | RefSeq DB | |||
| Sample name | MGMRh | MGNRh | MGMRh | MGNRh | MGMRh | MGNRh |
| Total mapped reads | 790,310 | 318,187 | 7,413,129 | 6,118,123 | 4,878,689 | 4,058,863 |
| Species name 1,2 | ||||||
| Rahnella aquatilis | 8260 | 9 | 26,556 | 46 | 216,768 | 364 |
| Rahnella sp. WP5 | ND | ND | 89,230 | 86 | ND | ND |
| Rahnella sp. Y9602 | 37,445 | 35 | 12,208 | 25 | ND | ND |
| SUM | 45,705 | 44 | 127,994 | 157 | 216,768 | 364 |
| Serratia liquefaciens | 24,395 | 25 | 32,253 | 91 | ND | ND |
| Serratia proteamaculans | 267 | 0 | ND | ND | 7693 | 184 |
| Serratia plymuthica | 258 | 1 | 304 | 37 | 6042 | 289 |
| Serratia marcescens | 41 | 4 | 452 | 149 | 4184 | 1223 |
| Serratia rubidaea | ND | ND | 142 | 134 | ND | ND |
| Serratia sp. S4 | ND | ND | 229 | 0 | ND | ND |
| Serratia quinivorans | ND | ND | 227 | 0 | ND | ND |
| Serratia fonticola | 8 | 0 | 114 | 33 | 1047 | 134 |
| Serratia entomophila | 88 | 0 | ND | ND | ND | ND |
| Serratia odorifera | 65 | 0 | 83 | 54 | ND | ND |
| Serratia sp. 506_PEND | ND | ND | 102 | 0 | ND | ND |
| Serratia sp. SCBI | 52 | 2 | 15 | 0 | ND | ND |
| Serratia grimesii | 1 | 0 | 72 | 0 | ND | ND |
| SUM | 25,175 | 32 | 33,993 | 498 | 18,966 | 1830 |
1 Those values in bold plus labeled with red color represent the top species in the rhizospheric soil of the control cultivar MD12 (MGMRh). 2 Those species not listed in this table if their mapped read counts in two samples were less than 10 reads. 3 ND means “not detected”.