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Wen Xin Chen - One of the best experts on this subject based on the ideXlab platform.
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Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China
Applied and environmental microbiology, 2014Co-Authors: Yao Yao, En Tao Wang, Xin Hua Sui, Rui Wang, Wen Xin ChenAbstract:The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia.
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Bradyrhizobium arachidis sp nov isolated from effective nodules of arachis hypogaea grown in china
Systematic and Applied Microbiology, 2013Co-Authors: Rui Wang, Yue Li Chang, En Tao Wang, Xin Hua Sui, Xiao Xia Zhang, Wen Tao Zheng, Dan Zhang, Li Ya Zhang, Wen Xin ChenAbstract:Abstract Twenty-three bacterial strains isolated from root nodules of Arachis hypogaea and Lablab purpureus grown in five provinces of China were classified as a novel group within the genus Bradyrhizobium by analyses of PCR-based RFLP of the 16S rRNA gene and 16S–23S IGS. To determine their taxonomic position, four representative strains were further characterized. The comparative sequence analyses of 16S rRNA and six housekeeping genes clustered the four strains into a distinctive group closely related to the defined species Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, Bradyrhizobium huanghuaihaiense, Bradyrhizobium japonicum and Bradyrhizobium daqingense. The DNA–DNA relatedness between the reference strain of the novel group, CCBAU 051107T, and the corresponding type strains of the five mentioned species varied between 46.05% and 13.64%. The nodC and nifH genes of CCBAU 051107T were phylogenetically divergent from those of the reference strains for the related species. The four representative strains could nodulate with A. hypogaea and L. purpureus. In addition, some phenotypic features differentiated the novel group from the related species. Based on all the results, we propose a new species Bradyrhizobium arachidis sp. nov. and designate CCBAU 051107T (=CGMCC 1.12100T = HAMBI 3281T = LMG 26795T) as the type strain, which was isolated from a root nodule of A. hypogaea and had a DNA G + C mol% of 60.1 (Tm).
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Bradyrhizobium daqingense sp nov isolated from soybean nodules
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Jing Yu Wang, En Tao Wang, Hong Can Liu, Xin Hua Sui, Rui Wang, Wen Feng Chen, Yan Ming Zhang, Wen Xin ChenAbstract:Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA–DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774T and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622T, Bradyrhizobium yuanmingense CCBAU 10071T and Bradyrhizobium betae LMG 21987T, further confirmed that this group represented a novel species. CCBAU 15774T shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774T was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774T ( = LMG 26137T = HAMBI 3184T = CGMCC 1.10947T) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T m).
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Bradyrhizobium huanghuaihaiense sp nov an effective symbiotic bacterium isolated from soybean glycine max l nodules
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Yan Ming Zhang, En Tao Wang, Xin Hua Sui, Wen Feng Chen, Yunzeng Zhang, Yu Guang Zhou, Wen Xin ChenAbstract:In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium . They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S–23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94 % similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum , Bradyrhizobium liaoningense and ‘Bradyrhizobium daqingense’ originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303T ( = LMG 26136T = CGMCC 1.10948T = HAMBI 3180T) as the type strain. The DNA G+C content of strain CCBAU 23303T is 61.5 mol% (T m).
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Bradyrhizobium lablabi sp nov isolated from effective nodules of lablab purpureus and arachis hypogaea
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Yue Li Chang, Jing Yu Wang, En Tao Wang, Hong Can Liu, Xin Hua Sui, Wen Xin ChenAbstract:Five strains isolated from root nodules of Lablab purpureus and Arachis hypogaea grown in the Anhui and Sichuan provinces of China were classified as members of the genus Bradyrhizobium. These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of Bradyrhizobium jicamae PAC68T, Bradyrhizobium pachyrhizi PAC48T and Bradyrhizobium elkanii USDA 76T, respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S–23S rRNA intergenic spacer (IGS) and the recA, atpD and glnII genes, DNA–DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus Bradyrhizobium. Sequencing of nifH and nodC genes and cross-nodulation tests showed that the representative strains CCBAU 23086T, CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical nifH and nodC gene sequences and were all able to nodulate Lablab purpureus, Arachis hypogaea and Vigna unguiculata. Based upon these results, the name Bradyrhizobium lablabi sp. nov. is proposed for this novel species and strain CCBAU 23086T ( = LMG 25572T = HAMBI 3052T) is designated as the type strain. The DNA G+C mol% is 60.14 (T m).
Mariangela Hungria - One of the best experts on this subject based on the ideXlab platform.
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Bradyrhizobium mercantei sp nov a nitrogen fixing symbiont isolated from nodules of deguelia costata syn lonchocarpus costatus
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Mariangela Hungria, Luisa Caroline Ferraz HeleneAbstract:Some bacteria collectively known as rhizobia can establish symbiotic relationships and the N2-fixation process with several legumes used as green manure, in pastures and for wood production. Symbionts belonging to the genus Bradyrhizobium are predominant in the tropics, and an increasing number of studies report high genetic diversity within the genus. We performed a polyphasic study with two strains belonging to the genus Bradyrhizobium – SEMIA 6399T and SEMIA 6404–isolated from root nodules of Deguelia costata (syn. Lonchocarpus costatus), an important legume native to eastern Brazil. In general, sequences of the 16S rRNA gene were highly conserved in members of the genus Bradyrhizobium , and the two strains were positioned in the Bradyrhizobium elkanii superclade, sharing 100 % nucleotide identity with Bradyrhizobium embrapense , Bradyrhizobium erythrophlei and Bradyrhizobium viridifuturi . However, multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed that the two strains belong to a distinct clade, sharing from 87.7 to 96.1 % nucleotide identity with related species of the genus Bradyrhizobium , being most closely related to B. viridifuturi . Average nucleotide identity of genome sequences between SEMIA 6399T and related species was lower than 92 %, below the threshold of species circumscription. nifH phylogeny clustered the SEMIA strains in a clade separated from other species of the genus Bradyrhizobium , and the nodD phylogeny revealed that SEMIA 6399T presents a more divergent sequence. Other phenotypic and genotypic traits were determined for the new group, and our data support the description of the SEMIA strains as representatives of Bradyrhizobium mercantei sp. nov.; SEMIA 6399T (=CNPSo 1165T=BR 6010T=U675T=LMG 30031T) was chosen as the type strain.
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Bradyrhizobium stylosanthis sp nov comprising nitrogen fixing symbionts isolated from nodules of the tropical forage legume stylosanthes spp
International Journal of Systematic and Evolutionary Microbiology, 2016Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Jean Luiz Simoes De Araujo, Luc Felicianus Marie Rouws, Jerri Edson Zilli, Marcia Maria Parma, Itamar Soares De Melo, Mariangela HungriaAbstract:The introduction of legumes and nitrogen-fixing bacteria in tropical areas under pasture is a key factor for improvement of soil fertility. However, there are still very few studies concerning the symbionts of tropical forage legumes. We performed a polyphasic study with three strains representing the genus Bradyrhizobium (BR 446T, BR 510 and BR 511) isolated from the tropical perennial forage legume of the genus Stylosanthes. On the basis of 16S rRNA gene sequences, the three strains showed highest similarity with B. huanghuaihaiense , and in the analysis of the intergenic transcribed spacer (ITS) they showed less than 93.4 % similarity to all described species of the genus Bradyrhizobium . Multilocus sequence analysis (MLSA) with three, four or five (dnaK, glnII, gyrB, recA and rpoB) housekeeping genes confirmed that the BR strains belong to a distinct clade, with <96.5 % nucleotide identity with other members of the genus Bradyrhizobium . Average nucleotide identity (ANI) of genome sequences between strain BR 446T and B. huanghuaihaiense was below the threshold for species circumscription (90.7 %). DNA-DNA hybridization resulted in ΔT m values over 6.7 °C with the most closely related species. Similarities among the BR strains and differences from other species were confirmed by rep-PCR analysis. Interestingly, the BR strains were grouped in the analysis of nifH and nodC genes, but showed higher similarity with B. iriomotense and B. manausense than with B. huanghuaihaiense , indicating a different evolutionary history for nitrogen-fixation genes. Morpho-physiological, genotypic and genomic data supported that these BR strains represent a novel species for which the name Bradyrhizobium stylosanthis sp. nov. is suggested. The type strain is BR 446T (=CNPSo 2823T=HAMBI 3668T=H-8T), isolated from Stylosanthes guianensis.
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Bradyrhizobium tropiciagri sp nov and Bradyrhizobium embrapense sp nov nitrogen fixing symbionts of tropical forage legumes
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Marcia Maria Parma, Itamar Soares De Melo, Mariangela Hungria, Ernesto Ormenoorrillo, Esperanza MartinezromeroAbstract:Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).
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Bradyrhizobium viridifuturi sp nov encompassing nitrogen fixing symbionts of legumes used for green manure and environmental services
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Mariangela Hungria, Luisa Caroline Ferraz Helene, Ernesto Ormenoorrillo, Esperanza Martinezromero, Marco A RogelAbstract:Symbiotic nitrogen-fixing bacteria, commonly called rhizobia, are agronomically important because they can provide significant amounts of nitrogen to plants and help in recovery of impoverished soils and improvement of degraded environments. In recent years, with advances in molecular techniques, several studies have shown that these bacteria have high levels of genetic diversity, resulting in taxonomic reclassifications and descriptions of new species. However, despite the advances achieved, highly conserved 16S ribosomal genes (16S rRNA) do not elucidate differences between species of several genera, including the genus Bradyrhizobium. Other methodologies, such as multilocus sequence analysis (MLSA), have been used in such cases, with good results. In this study, three strains (SEMIAs 690T, 6387 and 6428) of the genus Bradyrhizobium, isolated from nitrogen-fixing nodules of Centrosema and Acacia species, without clear taxonomic positions, were studied. These strains differed from genetically closely related species according to the results of MLSA of four housekeeping genes (dnaK, glnII, gyrB and recA) and nucleotide identities of the concatenated genes with those of related species ranged from 87.8 % to 95.7 %, being highest with Bradyrhizobium elkanii. DNA–DNA hybridization (less than 32 % DNA relatedness) and average nucleotide identity values of the whole genomes (less than 90.5 %) indicated that these strains represented a novel species, and phenotypic traits were determined. Our data supported the description of the SEMIA strains as Bradyrhizobium viridifuturi sp. nov., and SEMIA 690T ( = CNPSo 991T = C 100aT = BR 1804T = LMG 28866T), isolated from Centrosema pubescens, was chosen as type strain.
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phylogeny of nodulation and nitrogen fixation genes in Bradyrhizobium supporting evidence for the theory of monophyletic origin and spread and maintenance by both horizontal and vertical transfer
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Mariangela Hungria, Pâmela MennaAbstract:Bacteria belonging to the genus Bradyrhizobium are capable of establishing symbiotic relationships with a broad range of plants belonging to the three subfamilies of the family Leguminosae ( = Fabaceae), with the formation of specialized structures on the roots called nodules, where fixation of atmospheric nitrogen takes place. Symbiosis is under the control of finely tuned expression of common and host-specific nodulation genes and also of genes related to the assembly and activity of the nitrogenase, which, in Bradyrhizobium strains investigated so far, are clustered in a symbiotic island. Information about the diversity of these genes is essential to improve our current poor understanding of their origin, spread and maintenance and, in this study, we provide information on 40 Bradyrhizobium strains, mostly of tropical origin. For the nodulation trait, common (nodA), Bradyrhizobium-specific (nodY/K) and host-specific (nodZ) nodulation genes were studied, whereas for fixation ability, the diversity of nifH was investigated. In general, clustering of strains in all nod and nifH trees was similar and the Bradyrhizobium group could be clearly separated from other rhizobial genera. However, the congruence of nod and nif genes with ribosomal and housekeeping genes was low. nodA and nodY/K were not detected in three strains by amplification or hybridization with probes using Bradyrhizobium japonicum and Bradyrhizobium elkanii type strains, indicating the high diversity of these genes or that strains other than photosynthetic Bradyrhizobium must have alternative mechanisms to initiate the process of nodulation. For a large group of strains, the high diversity of nod genes (with an emphasis on nodZ), the low relationship between nod genes and the host legume, and some evidence of horizontal gene transfer might indicate strategies to increase host range. On the other hand, in a group of five symbionts of Acacia mearnsii, the high congruence between nod and ribosomal/housekeeping genes, in addition to shorter nodY/K sequences and the absence of nodZ, highlights a co-evolution process. Additionally, in a group of B. japonicum strains that were symbionts of soybean, vertical transfer seemed to represent the main genetic event. In conclusion, clustering of nodA and nifH gives additional support to the theory of monophyletic origin of the symbiotic genes in Bradyrhizobium and, in addition to the analysis of nodY/K and nodZ, indicates spread and maintenance of nod and nif genes through both vertical and horizontal transmission, apparently with the dominance of one or other of these events in some groups of strains.
En Tao Wang - One of the best experts on this subject based on the ideXlab platform.
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Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China
Applied and environmental microbiology, 2014Co-Authors: Yao Yao, En Tao Wang, Xin Hua Sui, Rui Wang, Wen Xin ChenAbstract:The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia.
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Bradyrhizobium arachidis sp nov isolated from effective nodules of arachis hypogaea grown in china
Systematic and Applied Microbiology, 2013Co-Authors: Rui Wang, Yue Li Chang, En Tao Wang, Xin Hua Sui, Xiao Xia Zhang, Wen Tao Zheng, Dan Zhang, Li Ya Zhang, Wen Xin ChenAbstract:Abstract Twenty-three bacterial strains isolated from root nodules of Arachis hypogaea and Lablab purpureus grown in five provinces of China were classified as a novel group within the genus Bradyrhizobium by analyses of PCR-based RFLP of the 16S rRNA gene and 16S–23S IGS. To determine their taxonomic position, four representative strains were further characterized. The comparative sequence analyses of 16S rRNA and six housekeeping genes clustered the four strains into a distinctive group closely related to the defined species Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, Bradyrhizobium huanghuaihaiense, Bradyrhizobium japonicum and Bradyrhizobium daqingense. The DNA–DNA relatedness between the reference strain of the novel group, CCBAU 051107T, and the corresponding type strains of the five mentioned species varied between 46.05% and 13.64%. The nodC and nifH genes of CCBAU 051107T were phylogenetically divergent from those of the reference strains for the related species. The four representative strains could nodulate with A. hypogaea and L. purpureus. In addition, some phenotypic features differentiated the novel group from the related species. Based on all the results, we propose a new species Bradyrhizobium arachidis sp. nov. and designate CCBAU 051107T (=CGMCC 1.12100T = HAMBI 3281T = LMG 26795T) as the type strain, which was isolated from a root nodule of A. hypogaea and had a DNA G + C mol% of 60.1 (Tm).
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Bradyrhizobium daqingense sp nov isolated from soybean nodules
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Jing Yu Wang, En Tao Wang, Hong Can Liu, Xin Hua Sui, Rui Wang, Wen Feng Chen, Yan Ming Zhang, Wen Xin ChenAbstract:Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA–DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774T and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622T, Bradyrhizobium yuanmingense CCBAU 10071T and Bradyrhizobium betae LMG 21987T, further confirmed that this group represented a novel species. CCBAU 15774T shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774T was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774T ( = LMG 26137T = HAMBI 3184T = CGMCC 1.10947T) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T m).
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Bradyrhizobium huanghuaihaiense sp nov an effective symbiotic bacterium isolated from soybean glycine max l nodules
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Yan Ming Zhang, En Tao Wang, Xin Hua Sui, Wen Feng Chen, Yunzeng Zhang, Yu Guang Zhou, Wen Xin ChenAbstract:In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium . They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S–23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94 % similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum , Bradyrhizobium liaoningense and ‘Bradyrhizobium daqingense’ originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303T ( = LMG 26136T = CGMCC 1.10948T = HAMBI 3180T) as the type strain. The DNA G+C content of strain CCBAU 23303T is 61.5 mol% (T m).
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Bradyrhizobium lablabi sp nov isolated from effective nodules of lablab purpureus and arachis hypogaea
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Yue Li Chang, Jing Yu Wang, En Tao Wang, Hong Can Liu, Xin Hua Sui, Wen Xin ChenAbstract:Five strains isolated from root nodules of Lablab purpureus and Arachis hypogaea grown in the Anhui and Sichuan provinces of China were classified as members of the genus Bradyrhizobium. These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of Bradyrhizobium jicamae PAC68T, Bradyrhizobium pachyrhizi PAC48T and Bradyrhizobium elkanii USDA 76T, respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S–23S rRNA intergenic spacer (IGS) and the recA, atpD and glnII genes, DNA–DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus Bradyrhizobium. Sequencing of nifH and nodC genes and cross-nodulation tests showed that the representative strains CCBAU 23086T, CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical nifH and nodC gene sequences and were all able to nodulate Lablab purpureus, Arachis hypogaea and Vigna unguiculata. Based upon these results, the name Bradyrhizobium lablabi sp. nov. is proposed for this novel species and strain CCBAU 23086T ( = LMG 25572T = HAMBI 3052T) is designated as the type strain. The DNA G+C mol% is 60.14 (T m).
Anne Willems - One of the best experts on this subject based on the ideXlab platform.
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Bradyrhizobium manausense sp nov isolated from effective nodules of vigna unguiculata grown in brazilian amazonian rainforest soils
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Flavia V Silva, Sofie E De Meyer, Jean Luiz Simoesaraujo, Tatiane Da Costa Barbe, Gustavo Ribeiro Xavier, G W Ohara, Julie Ardley, Norma Gouvea Rumjanek, Anne WillemsAbstract:Root nodule bacteria were trapped within cowpea (Vigna unguiculata) in soils with different cultivation histories collected from the Amazonian rainforest in northern Brazil. Analysis of the 16S rRNA gene sequences of six strains (BR 3351T, BR 3307, BR 3310, BR 3315, BR 3323 BR and BR 3361) isolated from cowpea nodules showed that they formed a distinct group within the genus Bradyrhizobium , which was separate from previously identified type strains. Phylogenetic analyses of three housekeeping genes (glnII, recA and rpoB) revealed that Bradyrhizobium huanghuaihaiense CCBAU 23303T was the most closely related type strain (96 % sequence similarity or lower). Chemotaxonomic data, including fatty acid profiles (predominant fatty acids being C16 : 0 and summed feature 8), the slow growth rate and carbon compound utilization patterns supported the assignment of the strains to the genus Bradyrhizobium . The results of DNA–DNA hybridizations, antibiotic resistance and physiological tests differentiated these novel strains from the most closely related species of the genus Bradyrhizobium with validly published names. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped the novel strains of the genus Bradyrhizobium together with Bradyrhizobium iriomotense strain EK05T, with 94 % and 96 % sequence similarity, respectively. Based on these data, these six strains represent a novel species for which the name Brabyrhizobium manausense sp. nov. (BR 3351T = HAMBI 3596T), is proposed.
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strains nodulating lupinus albus on different continents belong to several new chromosomal and symbiotic lineages within Bradyrhizobium
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2010Co-Authors: Encarna Velázquez, Anne Willems, Alvaro Peix, Raúl Rivas, Jose M Igual, Milagros Leonbarrios, Angel Valverde, Victor Gomis, Inne Gantois, Pedro F MateosAbstract:In this work we analysed different chromosomal and symbiotic markers in rhizobial strains nodulating Lupinus albus (white lupin) in several continents. Collectively the analysis of their rrs and atpD genes, and 16S-23S intergenic spacers (ITS), showed that they belong to at least four chromosomal lineages within the genus Bradyrhizobium. Most isolates from the Canary Islands (near to the African continent) grouped with some strains isolated on mainland Spain and were identified as Bradyrhizobium canariense. These strains are divided into two ITS subgroups coincident with those previously described from isolates nodulating Ornithopus. The remaining strains isolated on mainland Spain grouped with most isolates from Chile (American continent) forming a new lineage related to Bradyrhizobium japonicum. The strains BLUT2 and ISLU207 isolated from the Canary Islands and Chile, respectively, formed two new lineages phylogenetically close to different species of Bradyrhizobium depending on the marker analyzed. The analysis of the nodC gene showed that all strains nodulating L. albus belong to the biovar genistearum; nevertheless they form four different nodC lineages of which lineage C is at present exclusively formed by L. albus endosymbionts isolated from different continents.
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Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: Martha Helena Ramírez-bahena, Anne Willems, Alvaro Peix, Raúl Rivas, María Camacho, Dulce N Rodríguez-navarro, Pedro F Mateos, Eustoquio Martínez-molina, Encarna VelázquezAbstract:Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1% similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S-23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA-DNA hybridization analysis which revealed 21% genetic relatedness between strains PAC48T and PAC68T and 46% and 25%, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.
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Bradyrhizobium canariense sp nov an acid tolerant endosymbiont that nodulates endemic genistoid legumes papilionoideae genisteae from the canary islands along with Bradyrhizobium japonicum bv genistearum Bradyrhizobium genospecies alpha and bradyrhiz
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Anne Willems, Milagros Leonbarrios, A Jarabolorenzo, R Perezgaldona, Pablo Vinuesa, Claudia Silva, Dietrich Werner, Esperanza MartinezromeroAbstract:Highly diverse Bradyrhizobium strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, atpD, glnII and recA sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely Bradyrhizobium japonicum and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name Bradyrhizobium canariense is proposed. B. canariense populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric B. japonicum bv. genistearum strains in soils of the Canary Islands. B. canariense strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not Glycine species, whereas acid-sensitive B. japonicum soybean isolates such as USDA 6T and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic nifH and nodC sequences, the biovarieties genistearum and glycinearum for the genistoid legume and soybean isolates, respectively, were proposed. B. canariense bv. genistearum strains display an overlapped host range with B. japonicum bv. genistearum isolates, both sharing monophyletic nifH and nodC alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. B. canariense is the sister species of B. japonicum, as inferred from a maximum-likelihood Bradyrhizobium species phylogeny estimated from congruent glnII+recA sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel Bradyrhizobium genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for B. canariense is BTA-1T (=ATCC BAA-1002T=LMG 22265T=CFNE 1008T).
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Bradyrhizobium betae sp nov isolated from roots of beta vulgaris affected by tumour like deformations
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Raúl Rivas, Monique Gillis, Anne Willems, Pedro F Mateos, Jose Luis Palomo, Pablo Garciabenavides, Eustoquio Martinezmolina, Encarna VelázquezAbstract:Some varieties of sugar beet, Beta vulgaris, cultivated in northern Spain have large deformations that resemble the tumours produced by Agrobacterium species. In an attempt to isolate the agent responsible for these deformations, several endophytic slow-growing bacterial strains were isolated, the macroscopic morphology of which resembled that of Bradyrhizobium species. These strains were not able to produce tumours in Nicotiana tabacum plants and, based on phylogenetic analysis of their 16S rRNA, they are closely related to the genus Bradyrhizobium. Phenotypic and molecular characteristics of these strains revealed that they represent a species different from all Bradyrhizobium species previously described. Sequence analysis of the 16S–23S rDNA intergenic spacer region indicated that these novel strains form a homogeneous group, related to Bradyrhizobium japonicum, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense. DNA–DNA hybridization confirmed that these strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium betae sp. nov. is proposed. The type strain is PL7HG1T (=LMG 21987T=CECT 5829T).
Esperanza Martinezromero - One of the best experts on this subject based on the ideXlab platform.
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a genomotaxonomy view of the Bradyrhizobium genus
Frontiers in Microbiology, 2019Co-Authors: Ernesto Ormenoorrillo, Esperanza MartinezromeroAbstract:Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.
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Bradyrhizobium tropiciagri sp nov and Bradyrhizobium embrapense sp nov nitrogen fixing symbionts of tropical forage legumes
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Marcia Maria Parma, Itamar Soares De Melo, Mariangela Hungria, Ernesto Ormenoorrillo, Esperanza MartinezromeroAbstract:Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).
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Bradyrhizobium viridifuturi sp nov encompassing nitrogen fixing symbionts of legumes used for green manure and environmental services
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Mariangela Hungria, Luisa Caroline Ferraz Helene, Ernesto Ormenoorrillo, Esperanza Martinezromero, Marco A RogelAbstract:Symbiotic nitrogen-fixing bacteria, commonly called rhizobia, are agronomically important because they can provide significant amounts of nitrogen to plants and help in recovery of impoverished soils and improvement of degraded environments. In recent years, with advances in molecular techniques, several studies have shown that these bacteria have high levels of genetic diversity, resulting in taxonomic reclassifications and descriptions of new species. However, despite the advances achieved, highly conserved 16S ribosomal genes (16S rRNA) do not elucidate differences between species of several genera, including the genus Bradyrhizobium. Other methodologies, such as multilocus sequence analysis (MLSA), have been used in such cases, with good results. In this study, three strains (SEMIAs 690T, 6387 and 6428) of the genus Bradyrhizobium, isolated from nitrogen-fixing nodules of Centrosema and Acacia species, without clear taxonomic positions, were studied. These strains differed from genetically closely related species according to the results of MLSA of four housekeeping genes (dnaK, glnII, gyrB and recA) and nucleotide identities of the concatenated genes with those of related species ranged from 87.8 % to 95.7 %, being highest with Bradyrhizobium elkanii. DNA–DNA hybridization (less than 32 % DNA relatedness) and average nucleotide identity values of the whole genomes (less than 90.5 %) indicated that these strains represented a novel species, and phenotypic traits were determined. Our data supported the description of the SEMIA strains as Bradyrhizobium viridifuturi sp. nov., and SEMIA 690T ( = CNPSo 991T = C 100aT = BR 1804T = LMG 28866T), isolated from Centrosema pubescens, was chosen as type strain.
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Bradyrhizobium paxllaeri sp nov and Bradyrhizobium icense sp nov nitrogen fixing rhizobial symbionts of lima bean phaseolus lunatus l in peru
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: David Durán, Luis Rey, Juan Imperial, T Ruizargueso, Esperanza Martinezromero, Juan Mayo, Doris Zunigadavila, Ernesto OrmenoorrilloAbstract:A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of Bradyrhizobium lablabi CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus Bradyrhizobium . Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus Bradyrhizobium (≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus Bradyrhizobium were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.
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Bradyrhizobium canariense sp nov an acid tolerant endosymbiont that nodulates endemic genistoid legumes papilionoideae genisteae from the canary islands along with Bradyrhizobium japonicum bv genistearum Bradyrhizobium genospecies alpha and bradyrhiz
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Anne Willems, Milagros Leonbarrios, A Jarabolorenzo, R Perezgaldona, Pablo Vinuesa, Claudia Silva, Dietrich Werner, Esperanza MartinezromeroAbstract:Highly diverse Bradyrhizobium strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, atpD, glnII and recA sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely Bradyrhizobium japonicum and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name Bradyrhizobium canariense is proposed. B. canariense populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric B. japonicum bv. genistearum strains in soils of the Canary Islands. B. canariense strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not Glycine species, whereas acid-sensitive B. japonicum soybean isolates such as USDA 6T and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic nifH and nodC sequences, the biovarieties genistearum and glycinearum for the genistoid legume and soybean isolates, respectively, were proposed. B. canariense bv. genistearum strains display an overlapped host range with B. japonicum bv. genistearum isolates, both sharing monophyletic nifH and nodC alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. B. canariense is the sister species of B. japonicum, as inferred from a maximum-likelihood Bradyrhizobium species phylogeny estimated from congruent glnII+recA sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel Bradyrhizobium genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for B. canariense is BTA-1T (=ATCC BAA-1002T=LMG 22265T=CFNE 1008T).
