Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands

Vinuesa, Pablo; Silva, Claudia; Lorite, María J.; Izaguirre‐Mayoral, María Luisa; Bedmar, Eulogio J.; Martı́nez-Romero, Esperanza

doi:10.1016/j.syapm.2005.05.007

Cited by 169 publications

(102 citation statements)

References 46 publications

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“…In the genus Mesorhizobium, other genes have been used for phylogenetic purposes, such as dnaK (Stepkowski et al, 2003), atpD and recA (Vinuesa et al, 2005). The non-coding 16S-23S rRNA intergenic spacer (ITS) has also been used (Rivas et al, 2007).…”

Section: The Genus Mesorhizobiummentioning

confidence: 99%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene-and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches. INTRODUCTIONThe phylum Proteobacteria is composed of five classes, the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria (Garrity et al., 2005;Stackebrandt et al., 1988). By the end of 2008, more than 380 complete genomes of proteobacteria were available in public databases (http://www. ncbi.nlm.nih.gov/genomes/lproks.cgi). Alphaproteobacteria exhibit an enormous diversity in their morphological and metabolic characteristics and the class is presently recognized solely as a clade in the 16S rRNA gene-based phylogeny (Stackebrandt et al., 1988). Based on 16S rRNA gene trees, the Alphaproteobacteria has been divided into seven orders: Caulobacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Parvularculales (Kersters et al., 2006). The Alphaproteobacteria includes important bacteria tha...

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Section: The Genus Mesorhizobiummentioning

confidence: 99%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…A year later, Zeigler (2003) found that a smaller number of genes, or even a single, carefully selected core gene, can equal or even surpass the precision of DNA-DNA reassociation for the quantification of genome relatedness and assigning related bacteria to the correct species. The taxonomic potential of the MLSA technique, confirmed by DNA-DNA relatedness, has allowed the assignment of many nodule bacteria into species (Martens et al, 2008;Merabet et al, 2010;Rincó n-Rosales et al, 2009;Vinuesa et al, 2005). The MLSA technique has also been applied for rapid and reliable species identification in other bacterial genera, e.g.…”

Section: Resultsmentioning

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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“…The plants were grown at 25 8C in the growth room with a 16/8 h light/ dark photoperiod. Furthermore, the presence of nifH and nodC genes was assessed by PCR amplification with the primers and conditions as described by Laguerre et al (2001), Lin et al (2009) and Vinuesa et al (2005). After 6 weeks of culturing, strain PC004 T did not form any nodules on the tested plants, including the original host, which suggested that it is a non-nodulating endophyte.…”

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confidence: 99%

Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei

Boonsnongcheep

Prathanturarug

Takahashi

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan A Gram-stain-negative, rod-shaped, motile bacterium, PC004 T , was isolated from root nodules of the Thai medicinal plant Pueraria candollei var. candollei. 16S rRNA gene sequence analysis indicated that the strain is phylogenetically related to species in the genus Rhizobium, showing highest similarity (96.6 %) with Rhizobium mesosinicum HAMBI 3194 T . The phylogenetic tree reconstructed based on 16S rRNA gene sequences showed that strain PC004 T forms a cluster with Rhizobium petrolearium KCTC 23288 T . Based on atpD, gyrB and recA gene sequences, strain PC004 T also showed low similarity (,90 %) to reference strains. These phylogenetic data indicate that PC004 T may represent a novel species. Strain PC004 T also exhibited low DNA-DNA relatedness with R. mesosinicum HAMBI 3194 T (8.2 %) and R. petrolearium KCTC 23288 T (26.3 %). The DNA G+C content of strain PC004 T was 64 mol%, which is within the range reported for the genus Rhizobium. The major fatty acid of PC004 T was C 18 : 1 v7c with minor amounts of C 16 : 0 , C 16 : 0 3-OH, C 18 : 0 3-OH, C 18 : 1 2-OH, C 19 : 0 cyclo v8c and summed feature 2. The strain was able to grow at pH 12 and with up to 2 % (w/v) NaCl. Strain PC004 T did not nodulate five tested legumes and the nifH and nodC genes were not detected by PCR. Based on the physiological, chemotaxonomic and phenotypic data from this study, strain PC004 T represents a novel species of the genus Rhizobium, for which the name Rhizobium puerariae sp. nov. is proposed; the type strain is PC004 T (5BCC 73740 T 5NBRC 110722 T ).

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Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands

Cited by 169 publications

References 46 publications

dnaJ is a useful phylogenetic marker for alphaproteobacteria

dnaJ is a useful phylogenetic marker for alphaproteobacteria

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

Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei

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