International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of rhizobia and agrobacteria Minutes of the closed meeting, Granada, 4 September 2017

Lajudie, Philippe M. de; Young, J. Peter W.

doi:10.1099/ijsem.0.002974

Cited by 12 publications

(6 citation statements)

References 54 publications

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“…Average nucleotide identity (ANI) as an overall genome relatedness index is recommended to replace DNA–DNA hybridization methods for bacterial species delineation [14, 15, 25, 26]. We estimated ANI values for the complete genome sequence of 58S1 T and S23321 in pairwise comparisons with genome sequences of type strains of described Bradyrhizobium species available in public databases using the MUMmer (ANIm) algorithm implemented in the J-species web server version 3.0.20 [27].…”

Section: Genomic Characterizationmentioning

confidence: 99%

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

Wasai-Hara

Minamisawa

Cloutier

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.

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Section: Genomic Characterizationmentioning

confidence: 99%

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

Wasai-Hara

Minamisawa

Cloutier

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…It is also characterized by a comparatively large genome size (Supplementary Table S1). Nevertheless, more related strains are needed in order to propose ST15.13.057 as a new genomospecies according to the rules provided by the International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the Taxonomy of Rhizobia and Agrobacteria [105].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

Vargas Ribera,

Kim,

Venbrux

et al. 2024

Preprint

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Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacteriumtumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 579 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.

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“…Some of these species were isolated from plant tumours, such as Agrobacterium arsenijevicii [25] and Agrobacterium rosae [26], but others were isolated from legume nodules, such as Agrobacterium deltaense [55] and Agrobacterium salinitolerans [56], or plant wastes, such as Agrobacterium bohemicum [62]. In some of these works a strain named KB-105 (ATCC31113) from Agrobacterium viscosum was mentioned [12], nevertheless this species has not been officially proposed and moreover the strain KB-105, which is not a type strain, is currently included in a patent (U.S. Patent Number 4,028,185). Therefore, A. viscosum cannot be considered a valid species to date and then it has not been included in the present study.…”

Section: The Taxonomy Of Genus Agrobacterium From 2000 Onwardsmentioning

confidence: 99%

“…One of them, A. albertimagni, is more closely related to some Rhizobium species forming a rrs gene cluster (Fig. 1) that belong to neither Agrobacterium nor Rhizobium but to a separate genus [12,34]. Nevertheless, the reclassification of A. albertimagni in a new genus will need further studies since currently the genomes of several Rhizobium species belonging to this putative new genus are not available.…”

Section: The Taxonomy Of Genus Agrobacterium From 2000 Onwardsmentioning

confidence: 99%

History and current taxonomic status of genus Agrobacterium

Flores-Félix

Menéndez

Peix

et al. 2020

Systematic and Applied Microbiology

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The genus Agrobacterium was created a century ago by Conn who included it in the family Rhizobiaceae together with the genus Rhizobium. Initially, the genus Agrobacterium contained the non-pathogenic species Agrobacterium radiobacter and the plant pathogenic species Agrobacterium tumefaciens and Agrobacterium rhizogenes. At the end of the past century two new pathogenic species, Agrobacterium rubi and Agrobacterium vitis, were added to the genus. Already in the present century these species plus Agrobacterium larrymoorei were reclassified into genus Rhizobium. This reclassification was controversial and for a time both genus names were used when new species were described. Few years ago, after a taxonomic revision based on genomic data, the old species A. rhizogenes was maintained in the genus Rhizobium, the old species A. vitis was transferred to the genus Allorhizobium and several Rhizobium species were transferred to the genus Agrobacterium, which currently contains 14 species including the old species A. radiobacter, A. tumefaciens, A. rubi and A. larrymoorei. Most of these species are able to produce tumours in different plants, nevertheless the genus Agrobacterium also encompasses nonpathogenic species, one species able to nodulate legumes and one human pathogenic species. Taking into account that the species affiliations to five Agrobacterium genomospecies have not been determined yet, an increase in the number of species within this genus is expected in the near future.

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International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of rhizobia and agrobacteria Minutes of the closed meeting, Granada, 4 September 2017

Cited by 12 publications

References 54 publications

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

History and current taxonomic status of genus Agrobacterium

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