Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies

Eardly, Bertrand D.; Wang, F. S.; Berkum, Peter van

doi:10.1007/bf00035057

Cited by 46 publications

(34 citation statements)

References 11 publications

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“…Some strains switched branch between the two dendrograms, indicating that their ribosomal regions have a mosaic structure. This suggests that recombination has taken place during their evolution and supports the view of Eardly et al (4) that gene exchange has shaped the ribosomal genes in rhizobia. Also, the phylogenetic position of the R. galegae cluster is affected by the type of gene under study.…”

Section: Discussionsupporting

confidence: 84%

“…The longer fragment also contains enough conserved regions to avoid errors introduced by random noise. An interesting fact remains though, that part of the 16s gene and the IGS region of R. galegae have features in common with the corresponding regions of mesorhizobial ribosomal operons (4,21,32). A recombinational event during the evolution of these genera cannot be excluded.…”

Section: Discussionmentioning

confidence: 99%

“…A recombinational event during the evolution of these genera cannot be excluded. By comparing patterns of 16s nucleotide sequence polymorphism in members of both Aeromonadaceae and the Rhizobiaceae, Eardly et al (4) have shown results that demonstrate lateral transfer and recombination of these genes among species of the same genus. Another reason for the discrepancy between the 16s and 16s-IGS results might be explained by our observation that in many strains the IGS existed in multiple, variable copies, which rendered this region unsuitable for PCR-RFLP analysis.…”

Section: Discussionmentioning

confidence: 99%

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Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria

Terefework

Nick

Suomalainen

et al. 1998

International Journal of Systematic Bacteriology

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PCR-RFLP with nine restriction enzymes was applied to the 165 and 235 rRNA genes of 42 rhizobial and agrobacterial strains to determine the phylogenetic position of Rhizobium galegae and increase the understanding of the evolution of ribosomal operons. The strains were selected based on previous phylogenetic studies. PCR primers were designed so that they amplified a 2.3 kb fragment of the 23s rRNA gene (excluding the B8 loop). Universal primers rD1 and fD1 were used to amplify the full-length 165 rRNA. The RFLP analysis resulted in 27 and 32 different restriction patterns for 165 and 235, respectively. The RFLP patterns were transformed to genetic distances and dendrograms were constructed from the data using the unweighted pair group method with averages. The shapes of the dendrograms derived from the analysis of the 165 and 235 rRNA genes correlated well, with only a f e w strains having different positions. The 235 tree generally had deeper branching than the 165 tree, allowing better discrimination between species and strains. The combined data from the two analyses described 36 genotypes. The eight R. galegae strains formed a homogeneous cluster in all dendrograms. The RFLP analysis was confirmed by partial sequence analysis of the 165 rRNA gene (the first 800 bp), which correlated well with full-length 165 rRNA sequence analysis. The 165 data placed R. galegae near the genus Agrobacterium with Agrobacterium witis as its nearest neighbour, whereas in the 235 and the combined dendrograms it showed closer affinity to the genus Rhizobium.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria

Terefework

Nick

Suomalainen

et al. 1998

International Journal of Systematic Bacteriology

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“…For example, several reports have indicated that bacterial genomes may harbor more than a single copy of the 16S rRNA gene (2,6,12,48,67,69). Also, there is inferential evidence that ribosomal genes in certain bacteria or archeae undergo lateral transfer and genetic recombination (13,57,68,69,72). The possibility that 16S rRNA gene sequence divergence in single cells results from lateral transfer and recombination as well as mutation has important implications for evolutionary biology in bacterial populations and also for taxonomy and nomenclature.…”

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confidence: 99%

Discordant Phylogenies within the rrn Loci of Rhizobia

et al. 2003

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It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of ␣-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.Rhizobia are nitrogen-fixing bacterial symbionts of legumes that are of economic importance in low-input sustainable agriculture, agroforestry, and land reclamation. Descriptions of phenotypic and genetic variation among rhizobia have been extensive. Currently there are six genera of rhizobia, Allorhizobium, Azorhizobium, Bradyrhizobium, Rhizobium, Mesorhizobium, and Sinorhizobium, that have been proposed (65), and there is a report of a single species of Methylobacterium (of the family Methylobacteriaceae), Methylobacterium nodulans, which forms a symbiosis with specific species of Crotolaria (59). The primary criterion by which these genera are defined is analysis of 16S rRNA gene sequence (65).Sequencing the 16S rRNA gene has profoundly affected how relationships among the bacteria are portrayed (45). The 16S rRNA gene sequence is useful for this purpose because it is slowly evolving and the gene product is both universally essential and functionally conserved. However, basing bacterial phylogeny on 16S rRNA gene sequence variation not only presupposes that evolution throughout the genome progresses at a constant rate by mutation and Darwinian selection but also assumes that the evolution of the genome and of the 16S rRNA gene is strictly hierarchical. From a practical point of view this approach also requires each genome to harbor a single copy of the 16S rRNA gene or that multiple alleles within single genomes have identical sequences.Although seemingly convenient for c...

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“…It was also stated that the small-subunit (SSU) rRNA gene sequence similarity threshold of 98.7-99 % is a point at which DNA-DNA hybridization should be mandatory for testing the genomic taxonomic uniqueness of novel isolates (Stackebrandt & Ebers, 2006). The use of the 16S rRNA gene as the sole phylogenetic marker is currently being questioned, because of its presence in multiple copies within the genomes of some bacteria, evidence for intra-and intergeneric transfer of the 16S rRNA gene (including in rhizobia) and evidence for chimeric SSU rRNA gene sequences (Broughton, 2003;Eardly et al, 1996;Rajendhran & Gunasekaran, 2011).…”

Section: Introductionmentioning

confidence: 99%

Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization

Gnat

Małek

Oleńska

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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In this study, the phylogenetic relationship and taxonomic status of six strains, representing different phenons and genomic groups of Astragalus glycyphyllos symbionts, originating from Poland, were established by comparative analysis of five concatenated housekeeping gene sequences (atpD, dnaK, glnA, recA and rpoB), DNA-DNA hybridization and total DNA G+C content. Maximum-likelihood phylogenetic analysis of combined atpD, dnaK, glnA, recA and rpoB sequence data placed the studied bacteria into the clade comprising the genus Mesorhizobium. In the core gene phylograms, four A. glycyphyllos nodule isolates (AG1, AG7, AG15 and AG27) formed a cluster common with Mesorhizobium ciceri, whereas the two other A. glycyphyllos symbionts (AG17 and AG22) were grouped together with Mesorhizobium amorphae and M. septentrionale. The species position of the studied bacteria was clarified by DNA-DNA hybridization. The DNA-DNA relatedness between isolates AG1, AG7, AG15 and AG27 and reference strain M. ciceri USDA 3383 T was 76.4-84.2 %, and all these A. glycyphyllos nodulators were defined as members of the genomospecies M. ciceri. DNA-DNA relatedness for isolates AG17 and AG22 and the reference strain M. amorphae ICMP 15022 T was 77.5 and 80.1 %, respectively. We propose that the nodule isolates AG17 and AG22 belong to the genomic species M. amorphae. Additionally, it was found that the total DNA G+C content of the six test A. glycyphyllos symbionts was 59.4-62.1 mol%, within the range for species of the genus Mesorhizobium.

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Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies

Cited by 46 publications

References 11 publications

Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria

Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria

Discordant Phylogenies within the rrn Loci of Rhizobia

Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization

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