Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula

Schlesner, Heinz; Rensmann, Christina; Tindall, Brian J.; Gade, Dörte; Rabus, Ralf; Pfeiffer, Stefan; Hirsch, Peter

doi:10.1099/ijs.0.63113-0

Cited by 171 publications

(129 citation statements)

References 56 publications

(54 reference statements)

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“…In fact, some of the Chloroflexi detected in this study may have the potential to fix carbon in subseafloor sediment with or without dehalorespiration. Isolates or enrichments belonging to the phylum Planctomycetes also suggest heterotrophy with aerobic respiration or autotrophy with anaerobic ammonia oxidation by the Planctomycetes in the subseafloor biosphere 31,36) , but the phylotypes obtained in this study are also phylogenetically distant from these known groups 12) .…”

Section: Bacterial 16s Rrna Gene Communitiesmentioning

confidence: 58%

Subseafloor Microbial Communities in Methane Hydrate-Bearing Sediment at Two Distinct Locations (ODP Leg204) in the Cascadia Margin

et al. 2008

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The prokaryotic communities in deep subseafloor sediment collected during Ocean Drilling Program (ODP) Leg 204 from the South Hydrate Ridge (SHR) on the Cascadia Margin were analyzed by 16S rRNA gene clone sequencing and a fluorescent quantitative PCR technique. The microbial communities came from sites with contrasting geological characteristics on the SHR: sites 1244 and 1245 (located on the flank of the ridge, hydrate-rich sediment) and site 1251 (located on the slope basin of SHR, hydrate-poor sediment). The overall copy numbers of the 16S rRNA gene, and the proportion of archaeal 16S rRNA gene in all 16S rRNA gene community in sediment were larger on the slope basin than on the flank of the SHR. Archaeal community structure around the sulfate-methane transition zone at site 1251 (4.5 mbsf) was intensively investigated using two different PCR primer sets. A relatively abundant distribution of the 16S rRNA gene sequences related to mesophilic methanogen of the genus Methanoculleus was identified at a depth of 43.2 mbsf, and suggested that the methanogens occur in relatively shallow zones of sediment. This study demonstrated that the subseafloor microbial communities shown by 16S rRNA gene clone analyses were not directly associated with subseafloor methane hydrate deposits.

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Section: Bacterial 16s Rrna Gene Communitiesmentioning

confidence: 58%

Subseafloor Microbial Communities in Methane Hydrate-Bearing Sediment at Two Distinct Locations (ODP Leg204) in the Cascadia Margin

et al. 2008

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“…L. lactis was purchased from the DSMZ (Braunschweig, Germany) (DSM 4366) and grown at 30°C in LB medium. R. baltica SH1 T (35) and M. gryphiswaldense strain MSR-1 (34) were grown according to Schlesner et al (35) and Schübbe et al (38), respectively. For analysis of E. coli RNA, commercially available purified rRNA from E. coli MRE 600 (Boehringer, Ingelheim, Germany) was used.…”

Section: Methodsmentioning

confidence: 99%

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

Peplies

Lachmund

Glöckner

et al. 2006

Appl Environ Microbiol

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A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of ϳ5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.

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Section: Phylogenetic Analysismentioning

confidence: 99%

“…The topology of the subtree of planctomycete RNase P RNA sequences (Fig. 4) even from the genus Pirellula, as seems to be implied by the use of the tentative name 'Rhodopirellula baltica' for this strain by the group generating the genome sequence (Glöckner et al, 2003), and its formal proposal recently (Schlesner et al, 2004).The usefulness of RNase P RNA in differentiating planctomycetes is consistent with its utility for distinguishing members of the Chlamydiales (Herrmann et al, 2000) and consistency between 16S rRNA phylogenies and those derived from RNase P RNA has previously been found in studies of the cyanobacteria (Vioque, 1997) and the Chlamydiales (Herrmann et al, 2000). RNase P RNA gene sequences may prove useful for taxonomic investigations within planctomycete genera because of the relatively low similarity between homologous sequence regions relative to 16S rRNA, and the results of the present study are consistent with this view.…”

mentioning

confidence: 99%

Comparative analysis of ribonuclease P RNA of the planctomycetes

Butler

Fuerst

2004

International Journal of Systematic and Evolutionary Microbiology

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The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses. INTRODUCTIONRibonuclease P (RNase P) is the most widespread ribonuclease (Condon & Putzer, 2002), found in all organisms so far examined (Altman et al., 1989) except the bacterial species 'Aquifex aeolicus' (Condon & Putzer, 2002), and also found within the subcellular compartments of eukaryotes known to synthesize tRNA (Frank & Pace, 1998). It is one of the key enzymes involved in the processing of tRNA, responsible for the generation of the 59 termini of mature tRNA (Altman, 1975), via a single endonucleolytic cleavage (Deutscher, 1984). Due to its universal existence, it is most likely an ancient enzyme, possibly descended from the postulated 'RNA world', prior to the development of protein-directed catalysis (Brown & Pace, 1991;Jeffares et al., 1998). In bacteria, the RNase P molecule is composed of a small protein and a large RNA moiety (Pace & Brown, 1995), the latter of which is capable of in vitro catalysis (Guerrier-Takada et al., 1983). RNase P RNA molecules in bacteria can generally be divided into two structurally separate classes: type A, the most common form, and type B, which is found in the low-G+C Gram-positive bacteria . Type A is distinguished by the presence of helix P6 and the absence of helix P5.1. A third intermediate type, type C, has been observed in the green nonsulfur bacteria (Haas & Brown, 1998). RNase P RNA has proven useful for phylogenetic analysis of the Chlamydiales (Herrmann et al., 2000), Prochlorococcus (Schön et al., 2002), the LL-2,6-diaminopimelic acid-containing actinomycetes (Yoon & Park, 2000), Bartonella (Pitulle et al., 2002) and Vibrio core species (Maeda et al., 2001), among others.The phylum Planctomycetes (Garrity et al., 2001) comprises a distinct group of the do...

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Cited by 171 publications

References 56 publications

Subseafloor Microbial Communities in Methane Hydrate-Bearing Sediment at Two Distinct Locations (ODP Leg204) in the Cascadia Margin

Subseafloor Microbial Communities in Methane Hydrate-Bearing Sediment at Two Distinct Locations (ODP Leg204) in the Cascadia Margin

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

Comparative analysis of ribonuclease P RNA of the planctomycetes

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