TABLE 3.
nifH PCR product identities for type II methanotrophs and related bacteriaa
| Clone or culture | Methylocystis sp. LW2 | Methylocystis sp. LW5 | Methylosinus sp. LW3 | Methylosinus sp. LW4 | Methylosinus sp. LW8 | Methylosinus sp. PW1 | M. trichosporium OB3b | PO3120 AF059644 | PO3133 AF059645 | LG1120 AF212882 | LG1122 AF212884 | LG2369 AF212891 | H-RIC20 D26303 | AO12 AF016615 | B13 AF099789 | B. japonicum USDA 110 K01620 | P. rhizobiumK00487 | Rhizobium sp. ORS571 M16710 | H. seropedicaeZ54207 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Methylocystis sp. LW2 | 99.1 (108) | 94.4 (108) | 94.4 (108) | 95.4 (108) | 95.4 (108) | 95.4 (108) | 99.1 (108) | 95.4 (108) | 98.1 (108) | 98.1 (108) | 97.2 (108) | 95.2 (84) | 95.4 (108) | 93.5 (108) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 91.7 (108) | |
| Methylocystis sp. LW5 | 94.5 (325) | 94.4 (108) | 94.4 (108) | 95.4 (108) | 95.4 (108) | 95.4 (108) | 98.1 (108) | 94.4 (108) | 97.2 (108) | 97.2 (108) | 96.3 (108) | 95.2 (84) | 95.4 (108) | 92.6 (108) | 96.3 (108) | 95.4 (108) | 93.5 (108) | 92.6 (108) | |
| Methylosinus sp. LW3 | 89.5 (325) | 88.6 (325) | 95.4 (108) | 99.1 (108) | 99.1 (108) | 96.3 (108) | 95.4 (108) | 91.7 (108) | 94.4 (108) | 94.4 (108) | 93.5 (108) | 94.0 (84) | 93.5 (108) | 89.8 (108) | 92.6 (108) | 92.6 (108) | 90.7 (108) | 91.7 (108) | |
| Methylosinus sp. LW4 | 91.4 (325) | 91.1 (325) | 91.7 (325) | 96.3 (108) | 96.3 (108) | 99.1 (108) | 93.5 (108) | 89.8 (108) | 92.6 (108) | 92.6 (108) | 91.7 (108) | 95.2 (84) | 94.4 (108) | 89.8 (108) | 90.7 (108) | 90.7 (108) | 90.7 (108) | 91.7 (108) | |
| Methylosinus sp. LW8 | 90.2 (325) | 89.2 (325) | 98.5 (325) | 92.3 (325) | 100 (108) | 97.2 (108) | 96.3 (108) | 92.6 (108) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 95.2 (84) | 94.4 (108) | 90.7 (108) | 93.5 (108) | 93.5 (108) | 91.7 (108) | 92.6 (108) | |
| Methylosinus sp. PW1 | 90.4 (356) | 89.8 (325) | 98.2 (325) | 93.2 (325) | 98.5 (325) | 97.2 (108) | 96.3 (108) | 92.6 (108) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 95.2 (84) | 94.4 (108) | 90.7 (108) | 93.5 (108) | 93.5 (108) | 91.7 (108) | 92.6 (108) | |
| M. trichosporium OB3b | 92.6 (325) | 92.6 (325) | 91.1 (325) | 95.7 (325) | 91.7 (325) | 91.7 (325) | 94.4 (108) | 90.7 (108) | 93.5 (108) | 93.5 (108) | 92.6 (108) | 95.2 (84) | 95.4 (108) | 90.7 (108) | 91.7 (108) | 91.7 (108) | 91.7 (108) | 92.6 (108) | |
| PO3120 AF059644 | 88.0 (324) | 85.2 (324) | 84.9 (324) | 84.6 (324) | 85.5 (324) | 84.6 (324) | 85.2 (324) | 96.3 (108) | 99.1 (108) | 99.1 (108) | 98.1 (108) | 96.4 (84) | 94.4 (108) | 94.4 (108) | 96.3 (108) | 96.3 (108) | 95.4 (108) | 92.6 (108) | |
| PO3133 AF059645 | 85.8 (324) | 83.3 (324) | 82.7 (324) | 83.4 (325) | 83.3 (324) | 82.4 (324) | 83.0 (324) | 97.8 (324) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 91.7 (84) | 90.7 (108) | 90.7 (108) | 92.6 (108) | 92.6 (108) | 93.5 (108) | 88.9 (108) | |
| LG1120 AF212882 | 87.7 (324) | 84.9 (324) | 84.6 (324) | 84.3 (324) | 85.2 (324) | 84.3 (324) | 84.9 (324) | 99.7 (324) | 97.5 (324) | 98.1 (108) | 97.2 (108) | 96.4 (84) | 93.5 (108) | 93.5 (108) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 91.7 (108) | |
| LG1122 AF212884 | 87.7 (324) | 84.9 (324) | 84.6 (324) | 84.3 (324) | 85.2 (324) | 84.3 (324) | 84.9 (324) | 99.7 (324) | 97.5 (324) | 99.4 (324) | 97.2 (108) | 95.2 (84) | 93.5 (108) | 93.5 (108) | 95.4 (108) | 95.4 (108) | 94.4 (108) | 91.7 (108) | |
| LG2369 AF212891 | 87.0 (324) | 84.3 (324) | 84.0 (324) | 83.6 (324) | 84.6 (324) | 83.6 (324) | 84.3 (324) | 99.1 (324) | 96.9 (324) | 96.8 (324) | 98.8 (324) | 95.2 (84) | 92.6 (108) | 92.6 (108) | 94.4 (108) | 94.4 (108) | 93.5 (108) | 90.7 (108) | |
| H-RIC20 D26303 | 84.5 (252) | 85.7 (252) | 86.1 (252) | 86.5 (252) | 86.9 (252) | 86.5 (252) | 86.9 (252) | 86.9 (251) | 84.5 (251) | 86.9 (251) | 86.5 (251) | 86.5 (251) | 94.0 (84) | 92.9 (84) | 92.2 (115) | 93.0 (115) | 90.4 (115) | 91.3 (115) | |
| AO12 AF016615 | 85.8 (323) | 86.7 (323) | 85.8 (323) | 86.7 (323) | 86.7 (323) | 86.7 (323) | 87.9 (323) | 82.0 (323) | 81.1 (323) | 81.7 (323) | 81.7 (323) | 81.1 (323) | 85.7 (251) | 90.7 (108) | 91.7 (108) | 91.7 (108) | 91.7 (108) | 89.8 (108) | |
| B13 AF099789 | 84.9 (325) | 83.7 (325) | 82.2 (325) | 82.5 (326) | 83.4 (325) | 83.4 (326) | 82.8 (326) | 81.8 (324) | 80.9 (324) | 81.5 (324) | 81.5 (324) | 80.9 (324) | 78.0 (273) | 84.9 (324) | 91.7 (109) | 91.7 (109) | 92.7 (109) | 90.8 (109) | |
| B. japonicum USDA 110 K01620 | 79.6 (324) | 80.6 (324) | 79.9 (324) | 78.1 (324) | 79.6 (324) | 79.3 (324) | 79.0 (324) | 80.2 (323) | 79.3 (323) | 79.9 (323) | 79.9 (323) | 79.3 (323) | 77.9 (344) | 79.6 (324) | 79.1 (368) | 96.9 (294) | 92.5 (293) | 87.0 (293) | |
| P. rhizobiumK00487 | 81.8 (324) | 82.7 (324) | 80.6 (324) | 80.9 (324) | 80.9 (324) | 80.9 (324) | 82.1 (324) | 81.7 (323) | 80.8 (323) | 81.4 (323) | 81.4 (323) | 80.8 (323) | 79.9 (344) | 82.7 (324) | 77.2 (368) | 85.9 (1274) | 93.5 (293) | 86.3 (293) | |
| Rhizobium sp. ORS571 M16710 | 87.4 (325) | 88.9 (325) | 84.0 (324) | 87.1 (325) | 84.9 (325) | 84.6 (325) | 88.0 (325) | 85.5 (324) | 85.2 (324) | 85.2 (324) | 85.2 (324) | 84.6 (324) | 82.3 (344) | 83.6 (323) | 82.6 (368) | 78.5 (933) | 82.1 (914) | 86.3 (293) | |
| H. seropedicaeZ54207 | 85.8 (325) | 86.8 (325) | 84.6 (325) | 87.4 (325) | 85.5 (325) | 85.2 (325) | 86.8 (325) | 86.7 (324) | 84.6 (324) | 86.4 (324) | 86.4 (324) | 85.8 (324) | 82.0 (344) | 81.1 (323) | 81.8 (368) | 78.7 (890) | 77.8 (901) | 80.0 (935) |
a
Identities for the nifH PCR product obtained for pure culture type II methanotrophs, environmental clones, and related bacteria. Environmental amino acid identities with NifH from type II methanotroph pure cultures greater than identities with NifH from other bacteria are shown in bold. Also see Table 2, footnote a.