TABLE 2.
nifH PCR product identities for Methylomonas and related bacteriaa
| Clone or culture | M. methanica S1 | Methylomons sp. LW13 | Methylomonas sp. LW15 | H-RIC7 D26290 | H-RIC8 D26291 | H-RIC13 D26296 | H-RIC16 D26299 | H-RIC18 D26301 | H-RIC22 D26305 | H-RIC23 D26306 | LG1111 H AF212874 | LG1112 H AF212875 | K. pneumoniaeJ01740 | A. chroococcumM73020 | A. vinelandiiM11579 | V. diazotrophicusAF111110 | P. stutzeriAJ297529 | A. faecalisX96606 | M. purpuratumAF059648 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| M. methanica S1 | 98.2 (109) | 100 (109) | 97.6 (85) | 95.3 (85) | 96.5 (85) | 95.3 (85) | 97.6 (85) | 96.5 (85) | 96.5 (85) | 97.2 (109) | 97.2 (109) | 89.0 (109) | 90.0 (110) | 89.0 (109) | 89.9 (109) | 90.8 (109) | 89.0 (109) | 94.5 (109) | |
| Methylomons sp. LW13 | 93.6 (328) | 98.2 (109) | 95.3 (85) | 96.5 (85) | 98.8 (85) | 95.3 (85) | 97.6 (85) | 98.8 (85) | 98.8 (85) | 95.4 (109) | 95.4 (109) | 90.8 (109) | 91.8 (110) | 90.8 (109) | 91.7 (109) | 90.8 (109) | 89.0 (109) | 92.7 (109) | |
| Methylomonas sp. LW15 | 95.4 (328) | 92.7 (328) | 97.6 (85) | 95.3 (85) | 96.5 (85) | 95.3 (85) | 97.6 (85) | 96.5 (85) | 96.5 (85) | 97.2 (109) | 97.2 (109) | 89.0 (109) | 90.0 (110) | 89.0 (109) | 89.9 (109) | 90.8 (109) | 89.0 (109) | 94.5 (109) | |
| H-RIC7 D26290 | 88.6 (255) | 85.9 (255) | 88.2 (255) | 94.0 (116) | 94.0 (116) | 94.8 (116) | 95.7 (116) | 94.8 (116) | 93.1 (116) | 95.3 (85) | 95.3 (85) | 87.1 (116) | 87.2 (117) | 86.8 (91) | 86.2 (116) | 89.7 (116) | 86.8 (91) | 91.8 (85) | |
| H-RIC8 D26291 | 86.3 (255) | 84.3 (255) | 85.9 (255) | 87.4 (349) | 97.4 (116) | 97.4 (116) | 97.4 (116) | 98.3 (116) | 96.6 (116) | 91.8 (85) | 91.8 (85) | 88.8 (116) | 89.7 (117) | 89.0 (91) | 88.8 (116) | 90.5 (116) | 87.9 (91) | 90.6 (85) | |
| H-RIC13 D26296 | 86.7 (255) | 85.9 (255) | 85.9 (255) | 86.2 (348) | 90.2 (348) | 96.6 (116) | 98.3 (116) | 99.1 (116) | 98.3 (116) | 92.9 (85) | 92.9 (85) | 90.5 (116) | 91.5 (117) | 91.2 (91) | 90.5 (116) | 91.4 (116) | 89.0 (91) | 91.8 (85) | |
| H-RIC16 D26299 | 86.3 (255) | 84.7 (255) | 85.9 (255) | 87.4 (348) | 98.9 (349) | 90.2 (348) | 96.6 (116) | 97.4 (116) | 95.7 (116) | 92.9 (85) | 92.9 (85) | 88.8 (116) | 89.7 (117) | 89.0 (91) | 88.8 (116) | 90.5 (116) | 89.0 (91) | 91.8 (85) | |
| H-RIC18 D26301 | 91.8 (255) | 91.0 (255) | 91.0 (255) | 88.2 (348) | 92.0 (348) | 91.1 (348) | 92.0 (348) | 99.1 (116) | 97.4 (116) | 94.1 (85) | 94.1 (85) | 89.7 (116) | 90.6 (117) | 90.1 (91) | 89.7 (116) | 93.1 (116) | 90.1 (91) | 92.9 (85) | |
| H-RIC22 D26305 | 89.8 (255) | 89.8 (255) | 89.8 (255) | 84.5 (348) | 86.8 (348) | 89.1 (348) | 87.4 (348) | 89.1 (348) | 98.3 (116) | 92.9 (85) | 92.9 (85) | 90.5 (16) | 91.5 (117) | 91.2 (91) | 90.5 (116) | 92.2 (116) | 89.0 (91) | 91.8 (85) | |
| H-RIC23 D26306 | 89.8 (255) | 88.6 (255) | 88.2 (255) | 85.9 (348) | 87.9 (348) | 90.5 (348) | 87.9 (348) | 89.4 (348) | 87.6 (348) | 92.9 (85) | 92.9 (85) | 91.4 (116) | 92.3 (117) | 91.2 (91) | 92.2 (116) | 92.2 (116) | 89.0 (91) | 91.8 (85) | |
| LG1111H AF212874 | 85.3 (326) | 83.7 (326) | 84.0 (326) | 84.3 (255) | 81.6 (255) | 83.1 (255) | 82.4 (255) | 85.5 (255) | 83.1 (255) | 82.4 (255) | 97.2 (109) | 88.1 (109) | 89.1 (110) | 88.1 (109) | 89.0 (109) | 89.0 (109) | 88.1 (109) | 93.6 (109) | |
| LG1112H AF212875 | 86.2 (326) | 84.7 (326) | 85.6 (326) | 85.5 (255) | 84.3 (255) | 85.1 (255) | 85.1 (255) | 83.5 (255) | 83.1 (255) | 85.1 (255) | 89.3 (326) | 88.1 (109) | 89.1 (110) | 88.1 (109) | 89.0 (109) | 89.9 (109) | 88.1 (109) | 93.6 (109) | |
| K. pneumoniaeJ01740 | 74.8 (326) | 74.2 (326) | 74.5 (326) | 76.7 (347) | 75.8 (347) | 75.5 (347) | 76.1 (347) | 74.6 (347) | 74.6 (347) | 76.1 (347) | 76.1 (326) | 76.1 (327) | 88.7 (291) | 88.6 (289) | 91.3 (229) | 93.0 (158) | 87.7 (292) | 89.0 (109) | |
| A. chroococcumM73020 | 80.5 (329) | 80.2 (329) | 81.5 (329) | 81.1 (350) | 78.1 (352) | 79.4 (350) | 77.7 (350) | 78.6 (350) | 82.3 (350) | 78.0 (350) | 79.9 (329) | 81.2 (330) | 79.8 (875) | 95.5 (288) | 93.5 (230) | 96.2 (159) | 91.8 (291) | 91.8 (110) | |
| A. vinelandiiM11579 | 78.5 (326) | 79.4 (326) | 79.1 (326) | 80.4 (347) | 77.4 (349) | 79.5 (347) | 76.9 (347) | 77.8 (347) | 81.6 (347) | 78.4 (347) | 78.5 (326) | 80.7 (327) | 80.2 (868) | 88.0 (1286) | 93.0 (229) | 96.2 (158) | 91.3 (289) | 90.8 (109) | |
| V. diazotrophicusAF111110 | 81.0 (326) | 82.5 (326) | 81.0 (326) | 79.0 (348) | 77.6 (348) | 79.9 (348) | 78.2 (348) | 79.6 (348) | 77.6 (348) | 79.3 (348) | 79.5 (327) | 77.9 (326) | 78.5 (688) | 78.0 (691) | 77.8 (688) | 94.9 (158) | 92.6 (229) | 91.7 (109) | |
| P. stutzeriAJ297529 | 76.1 (326) | 76.4 (326) | 77.0 (326) | 78.7 (347) | 75.8 (347) | 77.8 (347) | 76.1 (347) | 77.8 (347) | 78.4 (347) | 76.1 (347) | 77.6 (326) | 78.3 (327) | 83.8 (475) | 80.3 (676) | 83.2 (612) | 77.5 (475) | 98.7 (158) | 92.7 (109) | |
| A. faecalisX96609 | 75.2 (326) | 75.5 (326) | 76.1 (326) | 77.8 (347) | 74.9 (347) | 77.2 (347) | 75.5 (347) | 76.7 (347) | 77.5 (347) | 76.1 (347) | 76.7 (326) | 78.0 (327) | 81.6 (870) | 81.9 (1071) | 83.5 (1005) | 75.3 (688) | 98.3 (1081) | 90.8 (109) | |
| M. purpuratumAF059648 | 75.5 (326) | 75.2 (326) | 75.5 (326) | 75.6 (254) | 72.0 (254) | 75.2 (254) | 72.4 (254) | 75.2 (254) | 74.4 (254) | 74.4 (254) | 78.2 (326) | 78.6 (327) | 84.4 (327) | 84.5 (330) | 85.0 (327) | 74.8 (326) | 88.4 (327) | 88.1 (327) |
a
Identities for the nifH PCR product obtained for pure cultures of Methylomonas strains, environmental clones, and related bacteria. Values above the diagonal are percent amino acid identity for the translated nifH products. Values below the diagonal are percent nucleotide identity. The number in parentheses is the number of the residues compared. Environmental amino acid identities with NifH from Methylomonas pure cultures greater than identities with NifH from other bacteria are shown in bold.