Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity

Ribeiro, Renan Augusto; Barcellos, Fernando Gomes; Thompson, Fabiano L.; Hungría, Mariangela

doi:10.1016/j.resmic.2009.03.009

Cited by 67 publications

(50 citation statements)

References 65 publications

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“…This MLSA approach combines congruent genomic data, excluding partitions with a significant level of incongruence, providing reliable genotypic characterization (Bull et al, 1993;Miyamoto & Fitch, 1995). Among the housekeeping genes used in MLSA for phylogenetic reconstructions of the order Rhizobiales are atpD, dnaK, glnII, gltA, glnA, recA, rpoB and thrC (Turner & Young, 2000;Gaunt et al, 2001;Weir et al, 2004;Stepkowski et al, 2005;Vinuesa et al, 2005a;Martens et al, 2007;Ribeiro et al, 2009), and the approach has already been used in studies with the genus Bradyrhizobium (Stepkowski et al, 2003(Stepkowski et al, , 2005Parker, 2004). One important example is the description of B. canariense, based on the phylogeny of atpD, glnII, recA and the ITS (Vinuesa et al, 2005a).…”

Section: Discussionmentioning

confidence: 99%

“…Multilocus sequence analysis (MLSA), which consists of examination of the sequences of several conserved housekeeping genes dispersed over at least 100 kb of the genome, has been proposed as a more accessible tool for assessing phylogeny and taxonomy of prokaryotes (Brett et al, 1998;Maiden et al, 1998;Godoy et al, 2003;Cooper & Feil, 2004). Using MLSA, Moulin et al (2004) observed high genetic diversity among Bradyrhizobium strains, and Ribeiro et al (2009) found strong concordance between MLSA of five housekeeping genes and DNA-DNA hybridization in Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.).…”

Section: Introductionmentioning

confidence: 99%

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Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes

Menna

Barcellos

Hungría

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

156

109

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Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes were obtained with MLSA of glnII, recA, atpD and dnaK. Greatest variability was observed when the atpD gene was amplified, and five strains related to B. elkanii revealed a level of variability never reported before. Another important observation was that a group composed of strains USDA 110, SEMIA 5080 and SEMIA 6059, all isolated from soybean, clustered in all six trees with high bootstrap support and were quite distinct from the clusters that included B. japonicum USDA 6 T . The results confirm that MLSA is a rapid and reliable way of providing information on phylogenetic relationships and of identifying rhizobial strains potentially representative of novel species. INTRODUCTIONThe genus Bradyrhizobium was created to accommodate bacteria capable of establishing N 2 -fixing symbioses with several leguminous species and characterized by slow growth and an alkaline reaction in culture media containing mannitol as a carbon source (Jordan, 1982). Based on 16S rRNA gene sequences, the genus Bradyrhizobium forms a clade in the Alphaproteobacteria, along with oligotrophic soil and aquatic bacteria such as Rhodopseudomonas palustris, Rhodoplanes roseus, Nitrobacter winogradskyi and Blastobacter denitrificans and pathogens such as Afipia species, among others (Saito et al., 1998;Willems et al., 2001a;van Berkum & Eardly, 2002;Sawada et al., 2003). Symbiotic Bradyrhizobium strains have been isolated from Abbreviations: ITS, intergenic transcribed spacer; MLSA, multilocus sequence analysis.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes

Menna

Barcellos

Hungría

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

156

109

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“…is closely related to R. tropici on the basis of 16S rRNA gene sequence analysis; however, it may be distinguished from R. tropici by phenotypic and genetic characteristics (Hungria et al, 2000;Ribeiro et al, 2009). A recent comparison of the genome of PRF 81 T to that of R. tropici CIAT 899 T highlighted the high similarity of their symbiotic plasmids, but considerable differences between the rest of their genomes, with low average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) (Ormeño-Orrillo et al, 2012).…”

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confidence: 99%

Rhizobium freirei sp. nov., a symbiont of Phaseolus vulgaris that is very effective at fixing nitrogen

Dall’Agnol

Ribeiro

Ormeño‐Orrillo

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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Common bean (Phaseolus vulgaris L.) can establish symbiotic associations with several Rhizobium species; however, the effectiveness of most strains at fixing nitrogen under field conditions is very low. PRF 81 T is a very effective strain, usually referred to as Rhizobium tropici and used successfully in thousands of doses of commercial inoculants for the common bean crop in Brazil; it has shown high rates of nitrogen fixation in all areas representative of the crop in the country. Here, we present results that indicate that PRF 81 T , although it belongs to the 'R. tropici group', which includes 10 Rhizobium species, R. tropici, R. leucaenae, R. lusitanum, R. multihospitium, R. miluonense, R. hainanense, R. calliandrae, R. mayense, R. jaguaris and R. rhizogenes, represents a novel species. Several morpho-physiological traits differentiated PRF 81 T from related species. Differences were also confirmed in the analysis of rep-PCR (sharing less than 45 % similarity with the other species), MLSA with recA, atpD and rpoB genes, and DNA-DNA hybridization. The novel species, for which we propose the name Rhizobium freirei sp. nov., is able to establish effective root nodule symbioses with Phaseolus vulgaris, Leucaena leucocephala, Leucaena esculenta, Crotalaria juncea and Macroptilium atropurpureum. The type strain is PRF 81 T (5CNPSo 122 T 5SEMIA 4080 T 5IPR-Pv81 T 5WDCM 440 T ).

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“…In our studies, we have identified other strains, including PRF 35 T , PRF 54, CPAO 1135 and H 52, which show high efficiency in N 2 fixation with common bean, and are classified as R. tropici (Hungria et al, 2000Mostasso et al, 2002;Pinto et al, 2007). However, our research group has accumulated evidence to indicate that these strains represent a distinct species (Mostasso et al, 2002;Chueire et al, 2003;Pinto et al, 2007;Ribeiro et al, 2009). …”

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confidence: 91%

Rhizobium paranaense sp. nov., an effective N2-fixing symbiont of common bean (Phaseolus vulgaris L.) with broad geographical distribution in Brazil

Dall’Agnol

Ribeiro

Delamuta

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Nitrogen (N), the nutrient most required for plant growth, is key for good yield of agriculturally important crops. Common bean (Phaseolus vulgaris L.) can benefit from bacteria collectively called rhizobia, which are capable of fixing atmospheric nitrogen (N 2 ) in root nodules and supplying it to the plant. Common bean is amongst the most promiscuous legume hosts; several described species, in addition to putative novel ones have been reported as able to nodulate this legume, although not always effectively in terms of fixing N 2 . In this study, we present data indicating that Brazilian strains PRF 35 T , PRF 54, CPAO 1135 and H 52, currently classified as Rhizobium tropici, represent a novel species symbiont of common bean. Morphological, physiological and biochemical properties differentiate these strains from other species of the genus Rhizobium, as do BOX-PCR profiles (less than 60 % similarity), multilocus sequence analysis with recA, gyrB and rpoA (less than 96.4 % sequence similarity), DNA-DNA hybridization (less than 50 % DNA-DNA relatedness), and average nucleotide identity of whole genomes (less than 92.8.%). The novel species is effective in nodulating and fixing N 2 with P. vulgaris, Leucaena leucocephala and Leucaena esculenta. We propose the name Rhizobium paranaense sp. nov. for this novel taxon, with strain PRF 35 T (5CNPSo 120 T 5LMG 27577 T 5IPR-Pv 1249 T ) as the type strain.

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Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity

Cited by 67 publications

References 65 publications

Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes

Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes

Rhizobium freirei sp. nov., a symbiont of Phaseolus vulgaris that is very effective at fixing nitrogen

Rhizobium paranaense sp. nov., an effective N2-fixing symbiont of common bean (Phaseolus vulgaris L.) with broad geographical distribution in Brazil

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