Skip to main content
. 2011 Jun 29;6(6):e21555. doi: 10.1371/journal.pone.0021555

Table 2. Identification of 16S rRNA gene terminal restriction fragments of class Deltaproteobacteria from Baltic Sea sediments.

T-RF size (bp) a with
HaeIII HhaI MspI RsaI
clone expectedb observedc observedd,e expectedb observedc observedd,e expectedb observedc observedd,e expectedb observedc observedd,e lowest rankf
JML-43 38 nd 29 92 88/90 88 504 503/505/506 504 487 487/488/490 488 Bacteriovorax (g)
JML-48 67 62/61 61 96 90/92 91 165 161/162 161 494 495 494 Desulfobacterium (g)
JML-70 71 71 65 83 76 78 200 201 199 441 440 440 Deltaproteobacteria (c)
Paila10-32 145 141 143 95 88/90/92 90 127 122 123 nd 490/492 491 Desulfomonile (g)
JML-67 178 nd 176 92 88/90 88 140 140 139 83 78/91 79 Deltaproteobacteria (c)
JML-37 183 nd 180 96 92 92 134 129/130 131/133g 57 52 50 Desulfobacteraceae (f)
JML-2 192 191/193 191/192h 94 88/90/92 90 163 162 163 213 211/213 212 Desulfobacterales (o)
JML-55 200 201/203 202 92 90/92 91 504 506/508 508 487 490/492 491 Desulfovibrio (g)
Paila10-52 204 203/205 203 94 88/90/92 90 143 nd 143 nd 490/492 492 Deltaproteobacteria (c)
JML-22 204 205/206 205 92 88/90/92 90 nd 510/511/512 512 225 226/227 226 Desulfobulbaceae (f)
JML-64 207 205/206 204 231 227 227 138 136/137 137 81 77/78 77 Desulfobacterales (o)
JML-5 208 205/206 205 96 88/90/92 90 69 62 62/64g 247 242/243 243 Desulfobacteraceae (f)
JML-29 208 205/206 206 379 378 378 165 165 164 57 52 51 Desulfobacteraceae (f)
Paila10-17 215 214/216 214 92 88/90 89 130 126/127/128 127 57 52 51 Desulfuromonadaceae(f)
Paila10-65 217 216/217 216 94 90/92 91 132 128/129/130 129 57 52/54 52 Desulfuromonadales(o)
JML-7 239 237/238 238 95 90/92 91 164 160/161/162 161 246 245/246 245 Desulfobacteraceae (f)
GF1-6 239 237/238 238 96 90/92 92 164 160/161/ 161 246 245/246 245 Desulfobacterium (g)
Paila10-20 240 235/237 236 94 88/90/92 90 209 206/209 208 nd 290 289 Deltaproteobacteria (c)
GF1-20 240 237/238 238 96 90/92 92 165 165/167 164/166g 247 246/245 245 Desulfobacterium (g)
GF1-41 254 254/255 254 92 88/90 88 130 126/127/128 127 463 462 463 Desulfuromusa (g)
Paila10-80 270 270/271 269 94 88/90/92 90 163 160/161/162 161 243 242/244 242 Desulfobulbaceae (f)
GF1-21 272 270/271 271 96 90/92 92 165 162/165 164 332 332 332 Desulfobacula (g)
GF1-39 272 270/271 271 96 90/92 92 165 162/165 162/163/164g nd 468/470/471 469/471g Desulfobacula (g)
GF1-34 423 423 423 96 90/92 92 165 165 164 332 332 332 Desulfobacula (g)

T-RF  =  terminal restriction fragment, nd  =  not detected.

a

Only those T-RFs that were identified with at least three restriction endonucleases are shown.

b

Expected T-RFs derived from virtual digestion of partial (approximately 400–500 bp) 16S rRNA gene clone sequences.

c

Observed T-RFs (between 50–700 bp) of 16S rRNA genes derived from terminal restriction fragment length polymorphism analysis of sediment samples.

d

Observed T-RFs (between 30–700 bp) of 16S rRNA genes derived from terminal restriction fragment length polymorphism analysis of 16S rRNA gene clones.

e

Shift of 0–2 bp between observed T-RFs from sediment samples and from 16S rRNA gene clones was allowed since repeats of restriction enzyme digestions of one 16S rRNA gene clone resulted 0–2 bp difference in lengths of observed T-RFs.

f

16S rRNA gene clone sequences used in virtual digestion were assigned to class level and the lowest rank (c  =  class, o  =  order, s  =  suborder, f  =  family, g  =  genus) using taxonomic Classifier (version 2.2, RDP training set 6) of Ribosomal Database Project (RDP) with 80% confidence threshold [39].

g

T-RFs of different size derived from one restriction enzyme digestion of one 16S rRNA gene clone.

h

T-RFs of different size derived from repeats of restriction enzyme digestions of one 16S rRNA gene clone.