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Stanton B Gelvin – One of the best experts on this subject based on the ideXlab platform.

  • editorial Agrobacterium biology and its application to transgenic plant production
    Frontiers in Plant Science, 2015
    Co-Authors: Hauhsuan Hwang, Stanton B Gelvin, Erhmin Lai

    The extraordinary Agrobacterium research story started from the search for the causative agent of crown gall disease more than 100 years ago. Agrobacterium tumefaciens was first isolated from grapevine galls in 1897 and later isolated from Paris daisy in 1907 (Cavara, 1897a,b; Smith and Townsend, 1907). The Agrobacterium infection mechanism involves processing and transfer of a specific DNA fragment (the transferred-DNA, T-DNA) from a bacterial tumor-inducing (Ti) plasmid. Transfer to the plant occurs via a type IV secretion system (T4SS), after which T-DNA is integrated into the plant host genome (Gelvin, 2010; Lacroix and Citovsky, 2013). This interkingdom DNA transfer leads to overproduction of the plant hormones auxin and cytokinin, resulting in tumors. The interkingdom DNA transfer ability of Agrobacterium and the possibility to replace the oncogenes in the T-DNA with genes of interest has made Agrobacterium-mediated transformation the most popular technique to generate transgenic plants. This Research Topic provides a collection of reviews and original research articles on Agrobacterium genes involved in bacterial physiology/virulence and plant genes involved in transformation and defense against Agrobacterium. A review by Kado (2014) provides a historical overview of how A. tumefaciens was first established as the cause of crown gall disease. In this review, Kado highlights key early plant pathology and milestone molecular biology studies leading to the conclusion that the expression of oncogenes in native T-DNA is the cause of tumor growth in plants. With the solid foundation of these pioneering discoveries, A. tumefaciens evolved from a phytopathogen to a powerful genetic transformation tool for plant biology and biotechnology research. The first complete genome sequence of an Agrobacterium species (A. tumefaciens C58) was completed in 2001 (Goodner et al., 2001; Wood et al., 2001). The 5.67-megabase genome of this strain carries one circular chromosome, one linear chromosome, and two megaplasmids: the Ti plasmid pTiC58 and a second plasmid, pAtC58. In the review by Platt et al. (2014), the properties, ecology, evolution, and complex interactions of these two A. tumefaciens megaplasmids are discussed. The costs and benefits to A. tumefaciens strains carrying the Ti plasmid and/or the pAtC58 plasmid are discussed and presented from an ecological and evolutionary perspective. Modeling predictions are presented for the relative cost and benefits to A. tumefaciens strains harboring the Ti and/or the pAtC58 plasmids determined by environmental resources. Conjugation and amplification of the Ti plasmid are regulated by the TraI/TraR quorum-sensing (QS) system and conjugal opines. Lang and Faure (2014) review current knowledge of the genetic networks and molecular basis of the A. tumefaciens quorum senssensing system. These authors also discuss the biological and ecological impact of the QS system on Ti plasmid conjugation, copy number, and interactions between Agrobacterium and host plants. During the initial interaction between Agrobacterium and plant cells, bacteria sense various plant-derived signals in the rhizosphere with the help of Ti plasmid-encoded virulence gene (vir gene) and chromosomal virulence gene (chv gene) products. The current knowledge of how A. tumefaciens senses and reacts to different plant-derived signals are summarized in the review article by Subramoni et al. (2014), which also discusses the mechanisms of how the plant hormones auxin, salicylic acid, and ethylene, affect bacterial viruvirulence. Finally, this review discusses the complexity and intricacy of Agrobacterium signaling pathways and the underlying regulatory mechanisms during the initial host cell recognition to maximize subsequent successful infection. In the original research article by Lin et al. (2014), the mechanistic regulation of the membrane sensor VirA protprotein is further dissected. VirA histidine kinase and the cytoplasmic response regulator VirG protein together play a central role in regulating vir gene expression in response to phenolics. Based on a homology model of the VirA linker region, various mutant and chimeric VirA proteins were generated and examined for their ability to induce VirB promoter activity. The ability of VirA to sense and respond to three separate input signals, phenolics, sugars, and environmental pH, plays a significant role in securing successful infection. Agrobacterium attachment to plant cells is an important early step in crown gall disease progprogression. Motile bacteria swim toward host cells and then physically interact with host cells to form aggregates and establish a multicellular bacterial community known as a biofilm. Various genetic and environmental factors that affect Agrobacterium attachment and biofilm formation are reviewed in the article by Heindl et al. (2014). The functions of different types of exopolysaccharides that constitute the biofilm and underlying mechanisms involving how the second messenger cyclic-di-GMP, the ChvG/ChvI system, phosphorus levels, and oxygen tension influence bacterial attachment and virulence are also summarized. In the review article by Matthysse (2014), early studies and current knowledge of the mechanisms of polar and lateral bacterial attachment are summarized. These two mechanisms both contribute to bacterial attachment. When the environmental calcium and phosphate levels and pH values are low, polar attachment predominates. In addition, the phospholipids (PLs), phosphatidylcholine (PC), and phosphate-free lipid ornithine lipids (OLs) contribute to Agrobacterium virulence. In the review by Aktas et al. (2014), the biosynthetic pathways and the physiological roles of these membrane lipids are summarized. The typical eukaryotic membrane lipilipid PC is not frequently found in bacteria, but it constitutes almost 22% of the Agrobacterium membrane lipilipid. Interestingly, PCs and OLs may play opposite roles in Agrobacterium virulence. The reduction of tumor formation in a PC-deficient Agrobacterium mutant may result from impaired vir gene expressions controlled by VirA/VirG. The absence of OLs in A. tumefaciens may decrease host defense responses and therefore cause earlier and larger tumor formation. Plant cells have a variety of receptors that recognize so-called microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), and subsequently activate plant defense responses, a process known as Pattern-recognition receptor-Triggered Immunity (PTI) (Boller and Felix, 2009; Boller and He, 2009). Agrobacteriium may utilize effectors to hijack plant systems and evade plant defense responses. Pitzschke (2013) reviews strategies used by Agrobacterium to turn plant defense responses to its own advantage. Infected plant cells initiate a mitogen-activated protein kinase signaling cascade that causes VIP1 (Agrobacterium VirE2-interacting protein 1) phosphorylation and translocation into the plant nucleus to induce defense gene expression. On the other hand, Agrobacterium may hijack VIP1 to help T-DNA enter the plant nucleus. Based on the current knowledge of plant defense responses against Agrobacterium infection, Pitzschke (2013) discusses several biotechnological approaches to increase transformation efficiency. In another review by Gohlke and Deeken (2014), early plant responses to Agrobacterium, including various defense responses, hypersensitive responses, and phytohormone level alterations are discussed. The alterations in plant morpmorphology, nutrient translocation, and metabolism caused by crown gall tumor formation are also reviewed. The authors summarize important genomic, epigenomic, transcriptomic, and metabolomic studies that reveal epigenetic changes associated with T-DNA integration and gall development. Subsequently, Hwang et al. (2015) review important pathogenic elicitors, host cell receptor molecules, and their downstream signal transduction pathways in host plants during the PAMP-triggered immune response. They highlight recent discoveries linking plant immuimmunity to endomembrane trafficking and actin dynamic changes. Effects of both the host physiology, including hormone levels, circadian clock, developmental stages, and environmental factors, including light exposure lengths and temperature, on plant defense responses and bacterial viruvirulence are reviewed and discussed. In nature, evidence of ancient horizontal gene transfers (HGT) from Agrobacterium to plants has been observed in the genera Nicotiana and Linaria. Sequences homologous to mikimopine-type Agrobacterium rhizogenes pRiA4 T-DNA were first discovered in the genome of untransformed tree tobacco, Nicotiana glauca, and named “cellular T-DNA” (cT-DNA; White et al., 1983). Matveeva and Lutova (2014) review cT-DNA organization, distribution, expression regulation, and a possible correlation with genetic tumor formation in Nicotiana species. They also review recent findings of cT-DNA in the genomes of Linaria species and in other dicotyledonous families. The authors suggest that plants maintaining cT-DNA in their genomes may potentially benefit microorganisms in the rhizosphere by secreting opines in the root zone. They also propose that footprints of ancient pRi T-DNA insertions in the plant genome may provide selective advantage to these plants. With this Research Topic we provide a platform for scientists to share their understanding of Agrobacterium biology and how Agrobacterium transforms plants. These contributions demonstrate how a highly active research community in plant and microbial sciences can elucidate important pathogenesis questions. Future research on Agrobacteium will continue to advance our understanding of plant-pathogen interactions, and provide new insights useful for plant genetic engineering.

  • Transgenic Arabidopsis plants expressing Agrobacterium tumefaciens VirD2 protein are less susceptible to Agrobacterium transformation.
    Molecular plant pathology, 2006
    Co-Authors: Hauhsuan Hwang, Kirankumar S Mysore, Stanton B Gelvin

    Agrobacterium tumefaciens causes crown gall disease on many plant species and can result in considerable economic losses. Here we report a new strategy to control crown gall disease by over-expressing Agrobacterium tumefaciens VirD2 protein in plants. Transgenic Arabidopsis plants over-expressing virD2 from constitutive or wound-inducible promoters are less susceptible to Agrobacterium-mediated transformation. Additionally, the transient introduction of an A. tumefaciens virD2 gene in tobacco BY-2 cells reduces subsequent Agrobacterium-mediated transformation.

  • transfer of t dna and vir proteins to plant cells by Agrobacterium tumefaciens induces expression of host genes involved in mediating transformation and suppresses host defense gene expression
    Plant Journal, 2003
    Co-Authors: Hongmei Jiang, R W Doerge, Stanton B Gelvin

    Agrobacterium tumefaciens is a plant pathogen that incites crown gall tumors by transferring to and expressing a portion of a resident plasmid in plant cells. Currently, little is known about the host response to Agrobacterium infection. Using suppressive subtractive hybrhybridization and DNA macroarrays, we identified numerous plant genes that are differentially expressed during early stages of Agrobacterium-mediated transformation. Expression profiling indicates that Agrobacterium infection induces plant genes necessary for the transformation process while simultaneously repressing host defense response genes, thus indicating successful utilization of existing host cellular machinery for genetic transformation purposes. A comparison of plant responses to different strains of Agrobacterium indicates that transfer of both T-DNA and Vir proteins modulates the expression of host genes during the transformation process.

Xavier Nesme – One of the best experts on this subject based on the ideXlab platform.

  • Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops
    Systematic and Applied Microbiology, 2018
    Co-Authors: Nemanja Kuzmanović, Joanna Pu\l Awska, Kornelia Smalla, Xavier Nesme

    The plant tumorigenic strain NCPPB 1650T isolated from Rosa\texttimeshybrida, and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus Agrobacterium. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, recA and rpoB housekeeping genes indicated that five strains studied form a novel Agrobacterium species. Their closest relatives were Agrobacterium sp. R89-1, Agrobacterium rubi and Agrobacterium skierniewicense. Authenticity of the novel species was confirmed by average nucleotide identity (ANI) and in silico DNADNA hybridization (DDH) comparisons between strains NCPPB 1650T and B20.3, and their closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. Whole-genome-based phylogeny further supported distinctiveness of the novel species, that forms together with A. rubi, A. skierniewicense and Agrobacterium sp. R89-1 a well-delineated sub-clade of Agrobacterium spp. named “rubi\textquotedblright. As for other species of the genus Agrobacterium, the major fatty acid of the strains studied was 18:1 w7c (73.4278.12%). The five strains studied were phenotypically distinguishable from other species of the genus Agrobacterium. Overall, polyphasic characterization showed that the five strains studied represent a novel species of the genus Agrobacterium, for which the name Agrobacterium rosae sp. nov. is proposed. The type strain of A. rosae is NCPPB 1650T (=DSM 30203T=LMG 230T=CFBP 4470T=IAM 13558T=JCM 20915T).

  • Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov.
    Systematic and Applied Microbiology, 2014
    Co-Authors: Seyed Abdollah Mousavi, Xavier Nesme, Céline Lavire, Niklas Wahlberg, Ludovic Vial, Lars Paulin, Philippe De Lajudie, Kristina Lindström

    The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genugenus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.

  • rapid and efficient identification of Agrobacterium species by reca allele analysis Agrobacterium reca diversity
    Microbial Ecology, 2010
    Co-Authors: Denis Costechareyre, Ali Rhouma, Céline Lavire, Perrine Portier, David Chapulliot, Franck Bertolla, Ali Boubaker, Yves Dessaux, Xavier Nesme

    The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one “former” Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.

Hiroyuki Sawada – One of the best experts on this subject based on the ideXlab platform.

  • a revision of rhizobium frank 1889 with an emended description of the genus and the inclusion of all species of Agrobacterium conn 1942 and allorhizobium undicola de lajudie et al 1998 as new combinations rhizobium radiobacter r rhizogenes r rubi r u
    International Journal of Systematic and Evolutionary Microbiology, 2001
    Co-Authors: J M Young, L D Kuykendall, Esperanza Martinezromero, A Kerr, Hiroyuki Sawada

    Rhizobium, Agrobacterium and Allorhizobium are genera within the bacterial family Rhizobiaceae, together with Sinorhizobium. The species of Agrobacterium, Agrobacterium tumefaciens (syn. Agrobacterium radiobacter), Agrobacterium rhizogenes, Agrobacterium rubi and Agrobacterium vitis, together with Allorhizobium undicola, form a monophyletic group with all Rhizobium species, based on comparative 16S rDNA analyses. Agrobacterium is an artificial genus comprising plant-pathogenic species. The monophyletic nature of Agrobacterium, Allorhizobium and Rhizobium and their common phenotypic generic circumscription support their amalgamation into a single genus, Rhizobium. Agrobacterium tumefaciens was conserved as the type species of Agrobacterium, but the epithet radiobacter would take precedence as Rhizobium radiobacter in the revised genus. The proposed new combinations are Rhizobium radiobacter, Rhizobium rhizogenes, Rhizobium rubi, Rhizobium undicola and Rhizobium vitis.

  • Proposal for Rejection of Agrobacterium tumefaciens and Revised Descriptions for the Genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes
    International journal of systematic bacteriology, 1993
    Co-Authors: Hiroyuki Sawada, Hiroyuki Ieki, Hiroshi Oyaizu, Satoshi Matsumoto

    The 16S rRNA sequences of seven representative Agrobacterium strains, eight representative Rhizobium strains, and the type strains of Azorhizobium caulinodans and Bradyrhizobium japonicum were determined. These strains included the type strains of Agrobacterium tumefaciens, Agrobacterium rhizogenes, Agrobacterium radiobacter, Agrobacterium vitis, Agrobacterium rubi, Rhizobium fredii, Rhizobium galegae, Rhizobium huakuii, Rhizobium leguminosarum, Rhizobium loti, Rhizobium meliloti, and Rhizobium tropici. A phylogenetic analysis showed that the 15 strains of Agrobacterium and Rhizobium species formed a compact phylogenetic cluster clearly separated from the other members of the alpha subclass of the Proteobacteria. However, Agrobacterium species and Rhizobium species are phylogenetically entwined with one another, and the two genera cannot be separated. In the Agrobacterium species, the strains of biovar 1, biovar 2, Agrobacterium rubi, and Agrobacterium vitis were clearly separated. The two biovars exhibited homogeneity in their phenotypic, chemotaxonomic, and phylogenetic characteristics, and two species should be established for the two biovars. We considered the nomenclature of the two biovars, and revised descriptions of Agrobacterium radiobacter(for the biovar 1 strains) and Agrobacterium rhizogenes(for the biovar 2 strains) are proposed. The name Agrobacterium tumefaciens is rejected because the type strain of this species was assigned to Agrobacterium radiobacter, and consequently the description of the genus Agrobacterium is revised.

Vitaly Citovsky – One of the best experts on this subject based on the ideXlab platform.

  • the roles of bacterial and host plant factors in Agrobacterium mediated genetic transformation
    The International Journal of Developmental Biology, 2013
    Co-Authors: Benoa T Lacroix, Vitaly Citovsky

    The genetic transformation of plants mediated by Agrobacterium tumefaciens represents an essential tool for both fundamental and applied research in plant biology. For a successful infection, culminating in the integration of its transferred DNA (T-DNA) into the host genome, Agrobacterium relies on multiple interactions with host-plant factors. Extensive studies have unraveled many of such interactions at all major steps of the infection process: activation of the bacterial viruvirulence genes, cell-cell contact and macromolecular translocation from Agrobacterium to host cell cytoplasm, intracellular transit of T-DNA and associated proteins (T-complex) to the host cell nucleus, disassembly of the T-complex, T-DNA integration, and expression of the transferred genes. During all these processes, Agrobacterium has evolved to control and even utilize several pathways of host-plant defedefense response. Studies of these Agrobacterium-host interactions substantially enhance our understanding of many fundamental cellular biological processes and allow improvements in the use of Agrobacterium as a gene transfer tool for biotechnology.

  • Agrobacterium: From Biology to Biotechnology – Agrobacterium : from biology to biotechnology
    , 2008
    Co-Authors: Tzvi Tzfira, Vitaly Citovsky

    Agrobacterium: A disease-causing bacterium.- A Brief History of Research on Agrobacterium Tumefaciens: 1900-1980s.- Agrobacterium and Plant BiotBiotechnology.- The Agrobacterium Tumefaciens C58 Genome.- Agrobacterium-Taxonomy of Plant-Pathogenic Rhizobium Species.- The Initial Steps in Agrobacterium Tumefaciens Pathogenesis: Chemical Biology of Host Recognition.- Agrobacterium-Host Attachment and Biofilm Formation.- Production of a Mobile T-DNA by Agrobacterium Tumefaciens.- Translocation of Oncogenic T-DNA and Effector Proteins to Plant Cells.- Intracellular Transport of Agrobacterium T-DNA.- Mechanisms of T-DNA integration.- Agrobacterium Tumefaciens-Mediated Transformation: Patterns of T-Dna Integration Into the Host Genome.- Function of Host Proteins in The Agrobacterium-Mediated Plant Transformation Process.- The Oncogenes of Agrobacterium Tumefaciens and Agrobacterium Rhizogenes.- Biology of Crown Gall Tumors.- The Cell-Cell Communication System of Agrobacterium Tumefaciens.- Horizontal GeneGene Transfer.- Agrobacterium-Mediated Transformation of Non-Plant Organisms.- The Bioethics and Biosafety of Gene Transfer.- Agrobacterium-Mediated Gene Transfer: A Lawyer’s Perspective.

  • Agrobacterium mediated genetic transformation of plants biology and biotechnology
    Current Opinion in Biotechnology, 2006
    Co-Authors: Tzvi Tzfira, Vitaly Citovsky

    Agrobacterium -mediated genetic transformation is the dominant technology used for the production of genetically modified transgenic plants. Extensive research aimed at understanding and improving the molecular machinery of Agrobacterium responsible for the generation and transport of the bacterial DNA into the host cell has resulted in the establishment of many recombinant Agrobacterium strains, plasmids and technologies currently used for the successful transformation of numerous plant species. Unlike the role of bacterial protproteins, the role of host factors in the transformation process has remained obscure for nearly a century of Agrobacterium research, and only recently have we begun to understand how Agrobacterium hijacks host factors and cellular processes during the transformation process. The identification of such factors and studies of these processes hold great promise for the future of plant biotbiotechnology and plant genetic engineering, as they might help in the development of conceptually new techniques and approaches needed today to expand the host range of Agrobacterium and to control the transformation process and its outcome during the production of transgenic plants.

Piotr Sobiczewski – One of the best experts on this subject based on the ideXlab platform.

  • Rapid and specific identification of four Agrobacterium species and biovars using multiplex PCR.
    Systematic and applied microbiology, 2005
    Co-Authors: Joanna Puławska, Anne Willems, Piotr Sobiczewski

    On the basis of 23S rRNA gene sequences, 1 universal forward and 4 taxon (species/biovar)-specific reverse primers were designed for multiplex PCR to aid in identification and differentiation of Agrobacterium rubi, Agrobacterium vitis and Agrobacterium biovars 1 and 2. In reactions with DNA of 119 bacterial strains belonging to: Agrobacterium, Allorhizobium, Mesorhizobium, Rhizobium, Sinorhizobium and Phyllobacterium, as well as phytopathogenic bacteria representing various genera, the primers developed for identification of A. vitis, A. rubi or Agrobacterium biovar 1 amplified only DNA of strains belonging to these taxa, producing fragments of the expected sizes: 478, 1006 and 184bp, respectively. However, in the case of the primer developed for identification of Agrobacterium biovar 2, the characteristic 1066bp PCR product was obtained not only with DNA of this biovar, but also with DNA of 3 atypical biovar 1 strains and some rhizobial strains. Differentiation between Agrobacterium biovar 2 and the other strains was possible using the restriction analysis of this product with endonuclease Alw26I. The method developed is an excellent tool for rapid classification of these 4 taxa of Agrobacterium.

  • Phylogenetic analysis of 23S rRNA gene sequences of. Agrobacterium, Rhizobium and Sinorhizobium strains.
    Systematic and Applied Microbiology, 2000
    Co-Authors: Joanna Puławska, Martine Maes, Anne Willems, Piotr Sobiczewski

    The phylogenetic relationship among twelve Agrobacterium, four Rhizobium, and two Sinorhizobium strains originating from various host plants and geographical regions was studied by analysis of the 23S rDNA sequences. The study included Agrobacterium strains belonging to biovars 1, 2 (with tumor- or hairy-root inducing and non-pathogenic strains), A. vitis, A. rubi; representative species of the Rhizobium genus: R. galegae, R. leguminosarum and R. tropici and Sinorhizobium meliloti strains. The phylogenetic analysis showed that within Agrobacterium, the biovar designation was reflected in the 23S rDNA similarity and that strains of Agrobacterium and Rhizobium are closely related to each other. The results suggest that the taxonomic definition of Agrobacterium and Rhizobium should be considered for revision and that the Agrobacteriumbiovar identity is probably a reliable taxonomic trait.