Table 2

Phylogenetic annotation of identified T-RFs
eTRFa(bp) dTRFa(bp) dTRF shiftedb(bp) Countsc(−) Relative contribution to T-RFd(%) Phylogenetic affiliatione Reference OTUf Reference GenBank accession numberg SW mapping scoreh(−) Normalized SW mapping scorei(−)
Aerobic granular sludge biofilms from wastewater treatment reactors
n.a. (32)j 39 34 550 70.6 F: Xanthomonadaceae 4015 GQ396926 386 0.960
(276) (35.0) (G: Thermomonas) (4045) (EU834762) (452) (0.983)
(128) (16.0) (G: Pseudoxanthomonas) (4035) (EU834761) (385) (0.955)
112 14.3 O: Flavobacteriales 1151 AY468464 434 1.000
46 5.9 F: Rhodobacteraceae 2718 AY212706 448 1.000
37 4.8 S: Rhodocyclus tenuis 3160 AB200295 363 0.917
18 2.3 O: Sphingobacteriales 1229 GU454872 394 0.990
5 0.6 C: Gammaproteobacteria 3370 AY098896 403 0.906
4 0.5 O: Rhizobiales 2549 EU429497 360 0.981
4 0.5 O: Myxococcales 3246 DQ228369 302 0.765
1 0.1 O: Bacteroidales 991 EU104248 180 0.636
194 198 193 10 90.9 G: Acidovorax 3011 AJ864847 384 1.000
1 9.1 F: Xanthomonadaceae 4035 EF027004 303 0.819
214 219 214 769 99.6 S: Rhodocyclus tenuis 3160 AB200295 371 0.949
1 0.1 G: Methyloversatilis 3158 DQ066958 368 0.958
1 0.1 G: Dechloromonas 3156 DQ413103 321 0.988
1 0.1 G: Nitrosomonas 3136 EU937892 278 0.753
220 225 220 50 92.6 O: Rhizobiales 2580 NR025302
(31) (57.0) (G: Aminobacter)
2 3.7 S: Rhodocyclus tenuis 3160 AB200295 206 0.703
1 1.9 F: Hyphomonadaceae 2656 AF236001 229 0.636
1 1.9 P: Firmicutes 2235 DQ413080 284 1.000
216 221 216 10 34.5 S: Rhodocyclus tenuis 3160 AF502230 296 0.773
8 27.6 G: Nitrosomonas 3136 GU183579 364 0.948
6 20.7 C: Anaerolineae 1317 EU104216 202 0.598
3 10.3 G: Methyloversatilis 3158 CU922545 360 0.909
1 3.4 G: Aminobacter 2580 L20802 281 0.829
1 3.4 G: Dechloromonas 3156 DQ413103 273 0.898
223 228 223 44 F: Intrasporangiaceae 418 AF255629
(G: Tetrasphaera)
15 24.6 F: Hyphomonadaceae 2656 AF236001 298 0.674
1 1.6 F: Microbacteriaceae 441 GQ009478 228 0.544
1 1.6 O: Acidimicrobiales 268 GQ009478 153 0.447
239 243 238 275 98.9 C: Gammaproteobacteria 3370 EU529737 446 0.982
2 0.7 G: Leptospira 4092 AB476706 350 0.926
1 0.4 P: Armatimonadetes 975 EU332819 275 0.846
249 253 249 9 100.0 S: Rhodocyclus tenuis 3160 AB200295 228 0.752
255 258 253 7 100.0 O: Sphingobacteriales 1171 FJ793188 355 0.989
260 263 258 16 94.1 G: Nitrospira 2360 GQ487996 389 0.982
1 5.9 O: Sphingobacteriales 1171 FJ536916 251 0.640
260 264 259 38 97.4 O: Sphingobacteriales 1170 EU104185 267 0.706
1 2.6 G: Nitrospira 2360 GQ487996 319 0.788
297 302 297 26 100.0 G: Herpetosiphon 1359 NC009972 339 0.867
307 311 306 38 97.4 P: Armatimonadetes 975 CU921283 218 0.472
1 2.6 O: Sphingobacteriales 1171 EU104210 196 0.525
321 323 318 17 100.0 G: Cytophaga 1208 EU104191 367 0.968
393 397 392 33 100.0 G: Bdellovibrio 3173 CU466777 262 0.663
Groundwater samples from chloroethene-contaminated aquifers
63 69 64 93 85.3 F: Methylococcaceae 3686 AB354618 432 0.915
14 12.8 F: Crenotrichaceae 3681 GU454947 290 0.816
1 0.9 F: Ectothiorhodospiraceae 3510 AM902494 168 0.542
1 0.9 P: candidate phylum OP3 2388 GQ356152 187 0.488
165 168 163 143 100.0 G: Dehalococcoides 1368 EF059529 448 0.953
190 193 191 12 54.6 F: Desulfobulbaceae 3177 AJ389624 379 0.945
4 13.6 F: Sphingomonadaceae 2880 AY785128 263 0.555
2 9.1 F: Erythrobacteraceae 2872 DQ811848 343 0.771
2 9.1 C: Alphaproteobacteria 2451 AY921822 337 0.926
1 4.6 F: Rhodospirillaceae 2793 AY625147 294 0.679
1 4.6 F: Rhodobiaceae 2641 AB374390 328 0.877
198 201 196 140 98.6 G: Desulfovibrio 3215 FJ810587 473 1.000
2 1.4 F: Comamonadaceae 3039 FN428768 311 0.814
210 214 209 233 98.3 F: Dehalococcoidaceae 1367 EU679418 262 0.665
2 0.8 O: Burkhorderiales 3009 AM777991 367 0.927
1 0.4 F: Spirochaetaceae 4130 EU073764 295 0.848
1 0.4 P: candidate phylum TM7 4379 DQ404736 277 0.723
216 221 216 1010 90.9 F: Gallionellaceae 3080 EU802012 353 0.869
94 8.5 G: Rhodoferax 3050 DQ628925 369 0.920
3 0.3 G: Methylotenera 3093 AY212692 291 0.744
1 0.1 G: Methyloversatilis 3158 GQ340363 296 0.765
1 0.1 F: Clostridiaceae 2005 AJ863357 338 0.833
1 0.1 C: Anaerolineae 1315 AB179693 229 0.511
1 0.1 C: Actinobacteria 949 EU644115 372 0.907
243 247 243 389 99.7 F: Dehalococcoidaceae 1367 EU679418 255 0.631
1 0.3 F: Anaerolinaceae 1321 AB447642 253 0.806

a Experimental (eT-RF) and digital T-RFs (dT-RF).

b Digital T-RF obtained after having shifted the digital dataset with the most probable average cross-correlation lag.

c Number of reads of the target phylotype that contribute to the T-RF.

d Diverse bacterial affiliates can contribute to the same T-RF.

e Phylogenetic affiliation of the T-RF (K: kingdom, P: phylum, C: class, O: order, F: family, G: genus, S: species). Only the last identified phylogenetic branch is presented here.

f Reference operational taxonomic unit (OTU) from the Greengenes public database related with the best SW mapping score. In the Greengenes taxonomy, OTU refer to terminal levels at which sequences are classified.

g GenBank accession numbers provided by Greengenes for reference sequences.

h Best SW mapping score obtained. SW scores consider nucleotide positions and gaps. The highest SW mapping score that can be obtained for a read is the length of the read itself.

i SW mapping score normalized by the read length, as an estimation of the percentage of identity.

j After having observed the presence of the dT-RF 34 bp, we returned to the raw eT-RFLP data and found an important eT-RF at 32 bp. However, Rossi et al. [8] considered that T-RFs below 50 bp are inconsistent and lacks of precision in sizing. This peak was therefore initially not taken into account in the original eT-RFLP profiles.

Weissbrodt et al.

Weissbrodt et al. BMC Microbiology 2012 12:306   doi:10.1186/1471-2180-12-306

Open Data