Proposal for Rejection of Agrobacterium tumefaciens and Revised Descriptions for the Genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes

Sawada, Hiroyuki; Ieki, Hiroyuki; Oyaizu, Hiroshi; Matsumoto, Satoshi

doi:10.1099/00207713-43-4-694

Cited by 220 publications

(162 citation statements)

References 38 publications

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“…The precise taxonomic position of the R. galegae strains is not yet clear. There is some evidence of their phylogenetic linkage to R. loti strains (36), but other authors showed them to be divergent from R. loti and demonstrated that they were more closely related to Agrobacten'urn species (23,31). The results of mobilization of symbiotic genes from R. galegae into Agrobactenum strains would seem to support the second finding (18).…”

Section: Discussionsupporting

confidence: 69%

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Numerical Taxonomy of Rhizobium Strains from Legumes of the Temperate Zone

Novikova¹,

Павлова²,

Vorobjev³

et al. 1994

International Journal of Systematic Bacteriology

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Phenotypic properties (growth characteristics, utilization of carbon and nitrogen sources, and intrinsic antibiotic resistance) of 53 Rhizobium strains isolated from root nodules of the temperate-zone legumes Astragalus spp. (29 strains), Oxytropis campanuhta (7 strains), Hedysarum alpinum (7 strains), Ononis awensis (3 strains), Glycyrrhiza spp. (4 strains), and Coronilh varia (3 strains) were compared with those of other Rhizobium, Bradyrhizobium, and Agrobacterium strains. The final matrix, containing 83 strains and 56 nonsymbiotic features, was used for computer cluster analysis. The dendrogram showed that the new strains of temperate-zone rhizobia formed a cluster separate from both Rhizobium and Bradyrhizobium spp. Two large groups of temperate-zone rhizobia were revealed. Group 1 included rhizobial strains originating from different geographical regions with a temperate climate, while group 2 included strains from the same geographical origin, South Siberia. The 'strains of recognized Rhizobium species were clustered, in general, with each other as expected from phylogenetic relatedness.Root nodule bacteria of the genera Rhizobium and Bradyrhizobium are a common microflora of temperate soils. These bacteria may interact with the roots of leguminous plants, inducing the formation of nodules in which the fixation of atmospheric nitrogen occurs. These bacteria are commonly used in agriculture for improvement of plant growth. The specificity of the interaction between rhizobia and legumes depends on many factors coded for by the host cultivar and bacterial genomes;. The main properties of a bacterial isolate can be described by its taxonomical position in relation to other strains. There are several Rhizobium species recognized at this time (10, 1.3, 24), and knowledge of rhizobial evolution and phylogeny obtained in recent studies allows the proposal of new rhizobial taxa (3,16,25). However, the current systematic description of the genus Rhizobium does not include many of the root nodule isolates from legumes of tropical (22, 37), arctic (21), and temperate (5, 12, 17) regions.The host plant specificities and phage sensitivities of Rhizobium strains from temperate-zone legume root nodules formed on Astragalus, Hedysamm, Glycywhiza, and Ononis plants were recently described (17). It was shown that these strains constitute a cross-inoculation group related to Rhizobium loti. The aim of the present work was to determine the cultural properties of these strains and to compare these properties with those of other Rhizobium species. MATERIALS AND METHODSBacterial strains. Bacterial strains used in this work are listed in Table 1. Bacteria were maintained on yeast extractmannitol (YEM) (29) agar slants at 4°C.Growth characteristics. The time necessary for full colony development on YEM agar (estimated here as a colony diameter of 2 mm) was determined. Bacterial growth on meat-peptone agar and reactions with litmus milk were determined as described earlier (11). The ability of strains to grow in the presence of 0,1...

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Section: Discussionsupporting

confidence: 69%

“…biovar 2 or R. Zegurninosarurn than it is to Agrobacten'urn sp. biovar 1 (14,16,23,31). Nevertheless, the symbiotic plasmid of CIAT 899 can be expressed in an A. tumefaciens C58 genetic background (15), and this fact suggests a degree of phenotypic relatedness between these two strains.…”

Section: Discussionmentioning

confidence: 99%

Numerical Taxonomy of Rhizobium Strains from Legumes of the Temperate Zone

Novikova¹,

Павлова²,

Vorobjev³

et al. 1994

International Journal of Systematic Bacteriology

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“…These groups include exceptionally slowly growing soybean rhizobia (personal communication) and groups of fast-growing rhizobia isolated from tropical regions Extensive studies on the phylogenetic relationships of rootand stem-nodulating bacteria in which workers have used 16s rRNA (ribosomal DNA) sequencing or rRNA-DNA hybridization have revealed that all previously described rhizobia belong to the alpha subclass of the Proteobacteria (7, 12, 13, 19, 23, [25][26][27][28][29][30] and that both the genus Rhizobium and the genus Bradyrhizobiurn are much more closely related to their corresponding nonsymbiotic relatives than to each other. Several distinct lineages have been identified in the genus Rhizobium, including the R. leguminosarum-R. tropici lineage, the R. meliloti-R. fredii lineage, the R. huakuii-R. loti lineage, and the R. galegae lineage (19,27). Considering the fact that Agrobacterium, Phyllobacterium, Mycoplana, Brucella, and Ochrobacterium species are embedded in Rhizobium lineages (19,(25)(26)(27), these Rhizobium lineages might represent separate genera (19,(25)(26)(27)(28)(29)(30).…”

mentioning

confidence: 99%

“…Several distinct lineages have been identified in the genus Rhizobium, including the R. leguminosarum-R. tropici lineage, the R. meliloti-R. fredii lineage, the R. huakuii-R. loti lineage, and the R. galegae lineage (19,27). Considering the fact that Agrobacterium, Phyllobacterium, Mycoplana, Brucella, and Ochrobacterium species are embedded in Rhizobium lineages (19,(25)(26)(27), these Rhizobium lineages might represent separate genera (19,(25)(26)(27)(28)(29)(30). The genus Bradyrhizobium constitutes a separate lineage and is closely related to Rhodopseudomonas palustrih, Blastobacter denitrifcans, and the genera Ajipia, and Nitrobacter (25,26).…”

mentioning

confidence: 99%

Characteristics of Rhizobium tianshanense sp. nov., a Moderately and Slowly Growing Root Nodule Bacterium Isolated from an Arid Saline Environment in Xinjiang, People's Republic of China

Chen

Wang

et al. 1995

International Journal of Systematic Bacteriology

173

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We performed a numerical analysis of 148 phenotypic characteristics of 20 strains of root nodule bacteria isolated from an arid saline desert soil in the Xinjiang region of northwestern People's Republic of China and compared these organisms with 28 Rhizobium and Bradyrhizobium strains obtained from different regions of the People's Republic of China and from other countries, including nine type strains of different species. All of the strains examined clustered into two groups at a similarity level of more than 63%. Group I included all of the previously described Rhizobium species and was divided into eight subgroups, which corresponded to previously described Rhizobium species, at a similarity level of more than 82%. Group I1 was divided into the following three subgroups at a similarity level of more than 80% Bradyrhizubium japonicum, a cluster containing 17 moderately and slowly growing strains isolated in the Xinjiang region, and a small subgroup containing three fast-growing strains. The generation times of the moderately and slowly growing strains were 5 to 15 h, and these organisms produced acid in medium containing mannitol. The DNA G+C contents of the members of this group ranged from 59 to 63 mol%. DNA-DNA hybridization experiments revealed that the levels of DNA homology among all of the moderately and slowly growing strains obtained from Xinjiang were more than 70% and that the levels of DNA homology between representative strains of this group and the type strains of all previously described species of root-and stem-nodulating bacteria were low. All of our experimental data indicated that the moderately and slowly growing rhizobia isolated from Xinjiang are members of a new species. Partial 16s rRNA gene sequencing of the type strain. A-1BS (= CCBAU3306), and a comparison of the resulting sequence with the sequences of previously described species revealed that strain A-1BS is closely related to Rhizobium loti, Rhizobium huakuii, and Rhizobium galegae, but not to B. japonicum and Azorhizobium caulinodans. On the basis of our results, we propose that the strains which we studied are members of a new species, Rhizobium tianshanense. The type strain, A-1BS (= CCBAU3306), has been deposited in the Culture Collection of Beijing Agricultural University, Beijing, People's Republic of China.At the present time, all bacteria that induce nodules on the roots of leguminous plants are assigned to three genera (8,14). The genus Rhizobium comprises a group of fast growers and includes eight species, Rhizobium leguminosarum, Rhizobium meliloti, Rhizobium loti (14), Rhizobium fredii (20), Rhizobium huakuii (2), Rhizobium galegae (15), Rhizobium tropici (16), and Rhizobium etli (21). Each of these species is associated with a group of host plants and is distinguished from the other species mainly on the basis of DNA relatedness values, 16s rRNA homology values, and some phenotypic characteristics. The genus Bradyrhizobium comprises a group of slow growers and contains one species, Bradyrhizobium japonicum, which i...

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“…have been divided into three distinct systematic units called biovar 1, biovar 2 and biovar 3 based on physiological characteristics. Later classification using rDNA sequences confirmed the biovar grouping as proposed by Sawada et al (1993), although the conventional pathovar grouping is still in common use.…”

Section: Introductionmentioning

confidence: 96%

Physical and gene maps of Agrobacterium biovar 2 strains and their relationship to biovar 1 chromosomes

et al. 2003

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Diverse types of genomic DNA organization have been found in Rhizobiaceae, especially among Agrobacterium species. Previous studies of Agrobacterium concentrated mainly on biovar 1 strains. Little attention has been given to biovar 2 strains. The biovar 2 genome consists of a large, circular chromosome and second megabase-sized replicon, as well as several plasmids. In this study two biovar 2 strains were analysed, A. rhizogenes (A. radiobacter) K84 and A. rhizogenes A4, by constructing physical maps of their chromosomes and mega-replicons. The maps revealed that in both strains their chromosomes consist of approximately 3·7 Mbp, while the mega-replicons are 2·6 Mbp circular DNAs. Gene mapping and comparative genomic analysis were performed based on the physical maps using Southern hybridization. It was found that rDNA, as well as analysed virulence and virulence-related genes, are present only on the chromosomes. The inter-chromosomal relationship between biovar 1 and biovar 2 strains was also analysed. Interestingly, there was a high similarity between the chromosomes of biovar 2 and the circular chromosomes of biovar 1, whereas similarity among the smaller megabase-sized replicons was restricted to each biovar. Based on these observations the possible relationship among large replicons in Agrobacterium biovars 1 and 2 is discussed.

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Proposal for Rejection of Agrobacterium tumefaciens and Revised Descriptions for the Genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes

Cited by 220 publications

References 38 publications

Numerical Taxonomy of Rhizobium Strains from Legumes of the Temperate Zone

Numerical Taxonomy of Rhizobium Strains from Legumes of the Temperate Zone

Characteristics of Rhizobium tianshanense sp. nov., a Moderately and Slowly Growing Root Nodule Bacterium Isolated from an Arid Saline Environment in Xinjiang, People's Republic of China

Physical and gene maps of Agrobacterium biovar 2 strains and their relationship to biovar 1 chromosomes

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