Characterization of diatom–cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences

ABSTRACT The level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16S rRNA-based methods. Furthermore, the occurrence of widespread horizontal gene transfer (HGT) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. For this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16S rRNA sequences were evaluated. Bacterial genomes display up to 15 operons and operon numbers up to 7 are commonly found, but ∼40% of the organisms analyzed have either one or two operons. Among the Archaea, a single operon appears to dominate and the highest number of operons is five. About 40% of sequences among 380 operons in 76 bacterial genomes with multiple operons were identical to at least one other 16S rRNA sequence in the same genome, and in 38% of the genomes all 16S rRNAs were invariant. For Archaea, the number of identical operons was only 25%, but only five genomes with 21 operons are currently available. These considerations suggest an upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment; however, the inclusion of genomes with a single rrn operon may lower this correction factor to ∼2.5. Divergence among operons appears to be small overall for both Bacteria and Archaea, with the vast majority of 16S rRNA sequences showing <1% nucleotide differences. Only five genomes with operons with a higher level of nucleotide divergence were detected, and Thermoanaerobacter tengcongensis exhibited the highest level of divergence (11.6%) noted to date. Overall, four of the five extreme cases of operon differences occurred among thermophilic bacteria, suggesting a much higher incidence of HGT in these bacteria than in other groups.

Download Full-text

Occurrence of diazotrophic bacteria in Araucaria angustifolia

Scientia Agricola ◽

10.1590/s0103-90162007000300015 ◽

2007 ◽

Vol 64 (3) ◽

pp. 303-304 ◽

Cited By ~ 4

Author(s):

Rafaela de Fátima Neroni ◽

Elke Jurandy Bran Nogueira Cardoso

Keyword(s):

16S Rrna ◽

Acetylene Reduction ◽

Araucaria Angustifolia ◽

Diazotrophic Bacteria ◽

Araucaria Forest ◽

Solid Media ◽

Reduction Assay ◽

Semi Solid ◽

Rrna Sequences ◽

16S Rrna Sequences

Araucaria angustifolia is an environmentally threatened tree and the whole biota of the Araucaria Forest should be investigated with the aim of its preservation. Diazotrophic bacteria are extremely important for the maintenance of ecosystems, but they have never been studied in Araucaria Forests. In this study, diazotrophic bacteria were isolated from Araucaria roots and soil, when grown in semi-specific, semi-solid media. The diazotrophic character of some recovered isolates could be confirmed using the acetylene reduction assay. According to their 16S rRNA sequences, most of these isolates belong to the genus Burkholderia.

Download Full-text

Identification of Streptococci to Species Level by Sequencing the Gene Encoding the Manganese-Dependent Superoxide Dismutase

Journal of Clinical Microbiology ◽

10.1128/jcm.36.1.41-47.1998 ◽

1998 ◽

Vol 36 (1) ◽

pp. 41-47 ◽

Cited By ~ 201

Author(s):

Claire Poyart ◽

Gilles Quesne ◽

Stephane Coulon ◽

Patrick Berche ◽

Patrick Trieu-Cuot

Keyword(s):

Superoxide Dismutase ◽

Pcr Assay ◽

Degenerate Primers ◽

Gene Encoding ◽

Genes Encoding ◽

Type Strains ◽

Internal Fragment ◽

Rrna Sequences ◽

16S Rrna Sequences

We have used a PCR assay based on the use of degenerate primers in order to characterize an internal fragment (sodAint ) representing approximately 85% of the genes encoding the manganese-dependent superoxide dismutase in various streptococcal type strains (S. acidominimus,S. agalactiae, S. alactolyticus, S. anginosus, S. bovis, S. constellatus,S. canis, S. cricetus, S. downei,S. dysgalactiae, S. equi subsp.equi, S. equi subsp. zooepidemicus,S. equinus, S. gordonii, S. iniae,S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis,S. pneumoniae, S. porcinus, S. pyogenes, S. salivarius, S. sanguis,S. sobrinus, S. suis, S. thermophilus, and S. vestibularis). Phylogenetic analysis of these sodAint fragments yields an evolutionary tree having a topology similar to that of the tree constructed with the 16S rRNA sequences. We have shown that clinical isolates could be identified by determining the positions of theirsodAint fragments on the phylogenetic tree of the sodAint fragments of the type species. We propose this method for the characterization of strains that cannot be assigned to a species on the basis of their conventional phenotypic reactions.

Download Full-text