TABLE 3.
Taxonomic identification of the single phylotypes only found in RNA-based SSCP fingerprints shown in Fig. 2b
| Phylotype | Sample(s)a (accession no.) | Taxonomic group | Closest 16S rRNA gene sequenceb (accession no.) | % Similarity | Closest described relativeb (accession no.) | % Similarity |
|---|---|---|---|---|---|---|
| 3 | ET, DW16 (DQ077600) | Acidobacteria | Uncultured clone GOUTB8 (AY050595) | 92.9 | NA | |
| 4 | DW15 (DQ077582) | Acidobacteria | Uncultured acidobacterial clone BSR3SF08 (AY690190) | 93.8 | NA | |
| 11 | ER1, ER2 (DQ077562) | Betaproteobacteria | Uncultured Acidovorax sp. clone SK224 (AY882778) | 96.5 | Comamonas terrigena (AJ430343) | 96.5 |
| 36 | DW15 (DQ077555) | Bacteriodetes | New gram-negative bacterium of CFB group (BD175053) | 98.5 | Riemerella anatipestifer (U60104) | 88.2 |
| 40 | GT (DQ077557) | Betaproteobacteria | Uncultured clone D115 (AY274125) | 86.0 | NA | |
| 41 | GT (DQ077592) | Betaproteobacteria | Nitrosospira briensis (AY123800) | 96.4 | Nitrosospira briensis (AJ298741) | 96.4 |
| 42 | Li, DW15 (DQ077580) | Betaproteobacteria | Nitrosomonas sp. isolate Is79A3 (AJ621026) | 99.2 | Nitrosomonas ureae (AF272414) | 97.2 |
| 43 | GT, Lb, Li, DW16, DW15 (DQ077596) | Betaproteobacteria | Nitrosospira briensis (AY123800) | 100 | Nitrosospira briensis (AJ298741) | 100 |
| 44 | GR1 (DQ077590) | Betaproteobacteria | Uncultured betaproteobacterium clone glen99_30 (AY150869) | 98.8 | Methylovorus mays (AY486132) | 93.4 |
| 45 | ET (DQ077595) | Betaproteobacteria | Uncultured clone TM08 (AY838516) | 100 | Burkholderia phenazinium (U96936) | 100 |
| 46 | GR1, ER1 (DQ077577) | Betaproteobacteria | Uncultured clone HB1 (AY996564) | 98.0 | Rhodoferax ferrireducens (AF435948) | 98.0 |
| 47 | GT (DQ077591) | Acidobacteria | Uncultured clone D14305 (AJ617855) | 95.2 | NA | |
| 48 | ER2 (DQ077598) | Gammaproteobacteria | Uncultured bacterium DSSD31 (AY328730) | 97.3 | Thioalkalispira microaerophila (AF481118) | 91.6 |
| 49 | Lb, DW15 (DQ077602) | Gammaproteobacteria | Uncultured gammaproteobacterium clone Sta2-95 (AY562363) | 99.0 | Methylocaldum gracile (U89298) | 92.4 |
| 50 | GR2 (DQ077588) | Verrucomicrobia | Uncultured clone 300G-H06 (AY661974) | 97.5 | Opitutus terrae (AJ229246) | 93.9 |
| 51 | Li (DQ077567) | Cyanobacteria | Uncultured clone B2C70D7 (AY957901) | 99.0 | Glaucocystis nostochinearumc (X82496) | 79.1 |
| 52 | Lb (DQ077587) | Chimera | NA | NA | ||
| 53 | GR1, GR2 (DQ077566) | Acidobacteria | Uncultured clone WD292 (AJ292589) | 95.7 | NA | |
| 54 | ET (DQ077599) | Alphaproteobacteria | Uncultured Caulobacteraceae clone KMD-0-40 (AY323816) | 100 | Phenylobacterium lituiforme (AY534887) | 97.2 |
| 55 | Li (DQ077572) | Alphaproteobacteria | Uncultured bacterium DSSF66 (AY328688) | 99.7 | Sphingomonas oligophenolica (AB018439) | 97.2 |
| 56 | ER2, ET, Li (DQ077581) | Acidobacteria | Uncultured clone LCSA21 (AJ608337) | 94.9 | NA | |
| 58 | Li (DQ077565) | Nitrospira | Uncultured clone LCo23 (AF337199) | 99.7 | “Nitrospira moscoviensis” (AF155155) | 95.5 |
| 61 | GT, DW16 (DQ077576) | Nitrospira | Uncultured Nitrospira-like DGGE gel band ESR BR 14 (AF540049) | 99.5 | “Nitrospira moscoviensis” (AF155155) | 98.4 |
| 64 | ET (DQ077571) | Planctomycetes | Uncultured Planctomycetes clone DSP21 (AJ290180) | 93.9 | Gemmata obscuriglobus (X81957) | 86.8 |
| 65 | ET (DQ077601) | Planctomycetes | Uncultured Planctomycetes clone DSP56 (AJ290192) | 95.5 | Pirellula marina (X62912) | 84.8 |
| 68 | GT, Li (DQ077597) | Planctomycetes | Uncultured Crater Lake bacterium CL500-3 (AF316767) | 96.4 | NA | |
| 70 | GR1, GR2 (DQ077569) | Bacteriodetes | Uncultured clone BIsi7 (AJ318176) | 92.8 | Pedobacter saltans (AJ438173) | 92.0 |
| 73 | GR1, GR2 (DQ077593) | Bacteriodetes | Uncultured clone TLM10/TLMdgge01 (AF534434) | 93.3 | Sejongia jeonii (AY553294) | 81.8 |
| 76 | GT (DQ077589) | Nitrospira | Uncultured ferromanganous bacterium MNF8 (AF293012) | 93.0 | “Nitrospira moscoviensis” (X82558) | 89.5 |
| 77 | Lb, Li, DW16, DW15 (DQ077559) | Betaproteobacteria | Uncultured bacterium DSSD99 (AY328796) | 98.3 | Acidovorax temperans (AF078766) | 97.3 |
| 78 | DW15 (DQ077558) | Bacteriodetes | Uncultured Bacteroidetes clone PS17 (DQ004377) | 88.0 | Flexibacter flexilis (AJ871243) | 86.9 |
| 79 | ER1 (DQ077568) | Bacteriodetes | Flexibacter aggregans (AB078038) | 89.3 | Flexibacter aggregans (AB078038) | 89.3 |
| 80 | ER1 (DQ077573) | Bacteriodetes | Uncultured bacterium FukuN24 (AJ289995) | 99.2 | Flexibacter sancti (AB078068) | 92.7 |
| 81 | GR1 (DQ077594) | Bacteriodetes | Uncultured clone C11-K8 (AJ421121) | 95.6 | Owenweeksia hongkongensis (AB125062) | 91.1 |
| 82 | GR1, DW16, DW15 (DQ077584) | Bacteriodetes | Uncultured gold mine bacterium D28 (AF337883) | 100 | Owenweeksia hongkongensis (AB125062) | 90.1 |
| 83 | ER1 (DQ077570) | Bacteriodetes | Uncultured bacterium DGGE gel band P17 (AY341117) | 98.4 | Pedobacter heparinus (AJ438172) | 95.4 |
| 84 | ER1 (DQ077575) | Betaproteobacteria | Uncultured betaproteobacterium clone BPC1_D08 (AY689932) | 96.1 | Gallionella ferruginea (L07897) | 95.4 |
| 86 | ER1 (DQ077563) | Gammaproteobacteria | Marinomonas primoryensis (AY771708) | 85.3 | Marinomonas primoryensis (AY771708) | 85.6 |
| 87 | GR1 (DQ077578) | Verrucomicrobia | Uncultured lake bacterium P38.38 (AY752101) | 98.3 | “Xiphinematobacter rivesi” (AF217461) | 90.8 |
| 88 | ER1 (DQ077583) | Acidobacteria | Uncultured forest soil bacterium clone DUNssu179 (AY913385) | 97.9 | NA | |
| 89 | ER1 (DQ077564) | Acidobacteria | Uncultured forest soil bacterium clone DUNssu338 (AY913514) | 96.8 | NA | |
| 90 | DW15 (DQ077585) | Acidobacteria | Uncultured Acidobacterium clone EB1129 (AY395448) | 95.3 | NA | |
| 91 | DW15 (DQ077556) | Cyanobacteria | Uncultured bacterium clone B1NR70D4 (AY957889) | 96.5 | Glaucocystis wittrockianac (X82495) | 83.1 |
| 92 | GR1 (DQ077560) | Alphaproteobacteria | Agricultural soil bacterium clone SC-I-27 (AJ252627) | 96.1 | NA | |
| 93 | DW16 (DQ077586) | Betaproteobacteria | Uncultured betaproteobacterium clone SNT3-94 (AY944210) | 92.2 | Rubrivivax gelatinosus (D16214) | 90.1 |
| 95 | Lb (DQ077561) | Betaproteobacteria | Uncultured bacterium FukuN108 (AJ289984) | 98.2 | Ferribacterium limneticum (Y17060) | 91.9 |
| 96 | DW16 (DQ077574) | Nitrospira | Uncultured Nitrospira-like DGGE gel band ESR BR 14 (AF540049) | 94.7 | “Nitrospira moscoviensis” (AF155155) | 92.7 |
a
Sample nomenclature is given in Fig. 2a.
b
NA, not applicable (i.e., the closest described relative has a similarity of <80%, as indicated in Materials and Methods).
c
Plastid of eukaryotic algae.