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. 2006 Sep;72(9):6257–6270. doi: 10.1128/AEM.00574-06

TABLE 3.

Archaeal and bacterial 16S rRNA gene clones generated in this study, in addition to previously published LCMS and marine group I clonesaa

Domain Clone GenBank accession no. Phylogenetic group Fragment size (bp)
HaeIII MspI BstuI
Archaea LC1022A-1 AY299516 LCMS 219 130 340
LC1149A-56 AY299515 LCMS 219* 130* 340*
LC1133A-9 AY760632 ANME-1 236* 96* 196*
LC1133A-17 DQ270605 ANME-1 235 96 197
FS197A-23 DQ270592 Thermococcales 154* 78 73
FS197A-30 DQ270593 Thermococcales 154 78 73
FS209A-41 DQ270596 Thermococcales 154 78 73
FS243A-6 DQ270598 Unc. Eury. 22 81 93
FS243A-60 DQ270602 Unc. Cren. 152 124 331
FS209A-10 DQ270595 Unc. Cren. 165 68 82
Bacteria LC1228B-35 DQ270650 Actinobacteria 187 426 184
LC1022B-39 DQ228573 Actinobacteria 191 105 472
LC1022B-1 DQ228574 Actinobacteria 309 455 96
LC1022B-27 DQ228572 Actinobacteria ND ND ND
LC1133B-64 DQ270644 Alpha-proteobacteria 188 399 58
LC1133B-90 DQ270648 Alpha-proteobacteria 188 400 58
LC1133B-8 DQ270640 Alpha-proteobacteria 188 400 58
LC1133B-74 DQ270646 Alpha-proteobacteria 183 429 72
LC1133B-45 DQ270642 Alpha-proteobacteria 163 410 167
LC1231B-170 DQ228567 Alpha-proteobacteria 188 400 58
LC1022B-48 DQ228566 Alpha-proteobacteria 188 399 58
LC1133B-23 DQ270615 Animal 152 288 26
LC1228B-46 DQ270625 Animal 151 286 26
LC1133B-24 DQ270616 Animal 155 107 358
LC1524B-50 DQ270636 Beta-proteobacteria 165 395 354
LC1537B-16 DQ270638 Beta-proteobacteria 165 440 354
LC1022B-30 DQ228559 Beta-proteobacteria 165 455 354
LC1537B-77 DQ272585 Chloroflexus 181 174 361
LC1231B-173 DQ228575 Chloroflexus 179 256 202
LC1408B-77 DQ270634 CFB 361 442 65
LC1446B-1 DQ270658 CFB 362 161 68
LC1524B-89 DQ270637 CFB 376 458 351
LC1228B-138 DQ270654 CFB 243 50 70
LC1133B-32 DQ270641 CFB 368 50 70
LC1022B-31 DQ228583 CFB 235 441 57
LC1228B-98 DQ270651 Desulfotomaculum 270 131* 77*
LC1537B-22 DQ270639 Desulfotomaculum 225 130 26
LC1404B-6 DQ270655 Epsilon-proteobacteria 769 431 355
LC1133B-68 DQ270645 Epsilon-proteobacteria 767 431 355
LC1228B-116 DQ270653 Epsilon-proteobacteria 767 431 355
LC1133B-58 DQ270643 Epsilon-proteobacteria 246 431 455
LC1408B-26 DQ270633 Epsilon-proteobacteria 855 431 355
LC1149B-14 DQ228557 Epsilon-proteobacteria 270 127 340
LC1149B-70 DQ228579 Epsilon-proteobacteria 1,133 162 349
LC1149B-104 DQ228555 Epsilon-proteobacteria 1,419 125 335
LC1231B-176 DQ228582 Epsilon-proteobacteria ND 436 360
LC1149B-9 DQ228581 Epsilon-proteobacteria ND ND 353
LC1149B-130 DQ228580 Epsilon-proteobacteria ND 162 349
LC1149B-115 DQ228556 Epsilon-proteobacteria ND 124 264
LC1408B-88 DQ270635 Firmicutes 267* 435^ 76*
LC1022B-45 DQ228570 Firmicutes 270 515 196
FS209A-1 DQ270594 Unc. Cren. 192 124 332
FS197A-14 DQ270591 Marine group I 214* 284* 460
FS243A-39 DQ270601 Marine group I 214 284 460
FS243A-7 DQ270590 Marine group I 214* 285* 461^
FS243A-90 DQ270604 Marine group I 214 284 460
LC1231A-51 AY505046 Marine group I 214 284 460
FS243A-20 DQ270599 Marine group II 208 191 260
FS243A-33 DQ270600 Marine group II 208 191 59
FS243A-89 DQ270603 Marine group II 315 191 130
FS243A-3 DQ270597 Marine group III 216 75 131
LC1022B-35 DQ228568 Firmicutes 236 28 196
LC1149B-139 DQ228571 Firmicutes 268 434 76
LC1022B-12 DQ228569 Firmicutes 269 114 195
LC1022B-45 DQ228570 Firmicutes 270 515 196
LC1537B-86 DQ270611 Marinomonas 212 449 69
LC1228B-136 DQ270627 Methylobacter 365 451 350
LC1133B-145 DQ270623 Methylobacter 367 453 477
LC1133B-37 DQ270617 Methylobacter 163 452 168
LC1446B-16 DQ270628 Methylobacter 289 459 176
LC1133B-99 DQ270621 Methylobacter 230 465 70
LC1446B-37 DQ270629 Methylobacter 279 449 70
LC1133B-5 DQ270612 Methylobacter 282 453 168
LC1133B-61 DQ270619 Methylobacter 214 451 70
LC1133B-86 DQ270620 Methylobacter 161 451 70
LC1231B-184 DQ228565 Methylobacter 215 452 70
LC1408B-19 DQ270606 Methylophaga 182 451 352
LC1446B-88 DQ270631 Methylophaga 282 453 352
LC1231B-11 DQ228564 Methylophaga 208 426 26
LC1443B-4 DQ270657 Nitrospira 357* 408* 520^
LC1228B-113 DQ270652 Nitrospira 355 406 518
LC1404B-28 DQ270656 Nitrospira 357* 408* 520^
LC1446B-146 DQ270662 Planctomycetes 247 88 74
LC1446B-77 DQ270660 Planctomycetes 217 150 84
LC1231B-20 DQ228576 Planctomycetes 173 103 20
LC1231B-166 DQ228578 Planctomycetes 220 438 217
LC1231B-5 DQ228577 Planctomycetes 245 134 112
LC1228B-91 DQ270626 Seep/hydrate 152 455 26
LC1133B-18 DQ270614 Seep/hydrate 216 104 72
LC1446B-28 DQ270659 Subsurface firm 297 157 40
LC1133B-75 DQ270647 Subsurface firm 297 157 40
LC1133B-108 DQ270649 Subsurface firm 171 151 211
LC1446B-39 DQ270630 Thiomicrospira 85 355 89
LC1537B-12 DQ270608 Thiomicrospira 184 455 72
LC1408B-58 DQ270607 Thiomicrospira 220 457 481
LC1537B-49 DQ270609 Thiomicrospira 184 454 170
LC1133B-148 DQ270624 Thiomicrospira 186 432 74
LC1133B-127 DQ270622 Thiomicrospira 185 455 73
LC1149B-99 DQ228561 Thiomicrospira 184 455 72
LC1022B-40 DQ228560 Thiomicrospira 297 255 86
LC1537B-81 DQ270610 Vibrio 174 464 181
a

See reference 65. The predicted terminal restriction fragment size for each restriction enzyme is generated by identifying the first restriction site for each enzyme 3′ to the fluorescently tagged forward primer. Fragment sizes were experimentally verified within ±2 bp (*) or ±4 bp (^). The absence of a restriction site present in the portion of the clone that was sequenced is indicated by “ND.” Unc. Eury., uncultured Euryarchaeota; Unc. Cren, uncultured Crenarchaeota; CFB, Cytophaga-Flavobacterium-Bacteroides.