Comparative Sequence Analysis of 23S rRNA from Proteobacteria

Ludwig, Wolfgang; Rosselló‐Móra, Ramon; Aznar, Rosa; Klugbauer, Sabine; Spring, Stefan; Reetz, Konstantin; Beimfohr, Claudia; Brockmann, Elke; Kirchhof, Gudrun; Dorn, Silvia; Bachleitner, Marianne; Klugbauer, Norbert; Springer, Nina; Lane, David; Nietupsky, Raymond; Weizenegger, Michael; Schleifer, Karl‐Heinz

doi:10.1016/s0723-2020(11)80388-7

Cited by 70 publications

(42 citation statements)

References 53 publications

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“…Sequence alignments were corrected manually by comparison with the secondary structure of Dichelobacter nodosus (y-Proteobacteria) 16s rRNA. A subset of 40 bacterial 16s rRNA sequences from the y-Proteobacteria, including the sequence from the type strain of Leucothvix rnucor, DSM 2157* (Ludwig et al, 1995) (Jukes & Cantor, 1969) were performed with the TREECON package ( Van de Peer & De Wachter, 1994) and trees were generated from distance matrices by the neighbour-joining method (Saitou & Nei, 1987). Parsimony analyses were accomplished with the DNAPARS program (Felsenstein, 1989) and maximum-likelihood analyses (Felsenstein,198 1) were done using fastDNAml .…”

Section: Methodsmentioning

confidence: 99%

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Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewatertreatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.

Howarth

Unz

Seviour

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

116

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Section: Methodsmentioning

confidence: 99%

“…16s rRNA analysis placed L. mucur DSM 2157T (Ludwig et al, 1995) as a deeply branching lineage at the base of the Thiothrix clade (Fig. 1).…”

Section: Eikelboom Type 021 N Bacteria Isolated From Different Continmentioning

confidence: 99%

Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewatertreatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.

Howarth

Unz

Seviour

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

116

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“…Unfortunately, our new finding also means that the published data on the 5S and 23S rRNA gene sequences of the DNA of the organism studied by Moreira et al (1994) and Moreira & Amils (1997), as well as reports on the genomic organization and chromosome size, must be treated with caution and merit further investigation (Moreira et al, 1994;Moreira & Amils, 1996Marin et al, 1997). The 23S rRNA gene of Thiomonas cuprina DSM 5495 T was sequenced independently by Ludwig et al (1995), using cells provided directly from Regensburg by Karl O. Stetter. This sequence (GenBank accession no.…”

mentioning

confidence: 94%

Reassessment of the phylogenetic relationships of Thiomonas cuprina

Kelly

Uchino

Huber

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö 5 (5DSM 5495 T ) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495 T 5NBRC 102145 T ) and strain Hö 5 maintained frozen in the Universitä t Regensburg for 23 years (5NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566 T and 'Thiomonas arsenivorans' DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.

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“…Microbial communities involved in wastewater treatment processes have been studied by FISH since 1993 (Wagner et al, 1993), and the procedure has led to the detection of several bacteria pivotal to success or failure of these processes (Crocetti et al, 2000(Crocetti et al, , 2002Juretschko et al, 1998;Rosselló -Mora et al, 1995;Schmid et al, 2000;Wagner et al, 1994a, b). Glycogen-accumulating organisms (GAOs) are considered important destabilizers of enhanced biological phosphorus removal (EBPR) due to their capacity to overgrow the organisms responsible for EBPR, the polyphosphate-accumulating organisms (PAOs).…”

Section: Introductionmentioning

confidence: 99%

Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation

et al. 2003

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The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium ‘Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 1027–1043 in the 23S rRNA and differ from each other by one nucleotide at position 1033. Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in ‘Candidatus C. phosphatis’. With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as ‘Candidatus C. phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a. However, none of the clones had the BET42a probe target (A at 1033). Non-canonical base-pairing between the 23S rRNA of ‘Candidatus C. phosphatis' with G at position 1033 and GAM42a (G–A) or BET42a (G–T) is likely to explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some ‘Candidatus C. phosphatis' cells, but also other bacteria. This demonstrates that there are bacteria in addition to ‘Candidatus C. phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.

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Comparative Sequence Analysis of 23S rRNA from Proteobacteria

Cited by 70 publications

References 53 publications

Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewatertreatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.

Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewatertreatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.

Reassessment of the phylogenetic relationships of Thiomonas cuprina

Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation

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