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Taxonomy browser (Agrobacterium tumefaciens)

Agrobacterium tumefaciens

Taxonomy ID: 358 (for references in articles please use NCBI:txid358)
current name
Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 (Approved Lists 1980) in [Skerman VBD et al. (1980)]
type strain of Agrobacterium tumefaciens: ATCC:23308, CFBP:2413, HAMBI:1811, ICMP:5856, BCCM/LMG:187, NCPPB:2437, IAM:12048, DSM:30205, personal::B6
homotypic synonym:
"Bacterium tumefaciens" Smith and Townsend 1907, effective name 1)
"Pseudomonas tumefaciens" (Smith and Townsend 1907) Duggar 1909, effective name 1)
"Phytomonas tumefaciens" (Smith and Townsend 1907) Bergey et al. 1923, effective name 1) in [Bergey DH et al. (1923)]
"Polymonas tumefaciens" (Smith and Townsend 1907) Lieske 1928, effective name 1)
includes:
Agrobacterium sp. ISSDS-827
Agrobacterium tumefaciens (TI PLASMID PTI15955)
Agrobacterium tumefaciens (TI PLASMID PTIA6NC)
Agrobacterium tumefaciens (TI PLASMID PTIACH5)
Agrobacterium tumefaciens (TI PLASMID PTIBO542)
Agrobacterium tumefaciens (TI PLASMID PTIC58)
Agrobacterium tumefaciens (TI PLASMID PTIT37)
Agrobacterium tumefaciens (TI PLASMID PTITM-4)
Agrobacterium tumefaciens (Ti plasmid pTib6s3)
Rhizobium sp. ISSDS-758
NCBI BLAST name: a-proteobacteria
Rank: species
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
heterotypic synonym
Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980)
type strain of Agrobacterium radiobacter: CCUG:3354, NCIMB:9042, DSM:30147, ATCC:19358, IFO:13532, IAM:12048, NBRC:13532, DSM:30147
homotypic synonym:
"Bacillus radiobacter" Beijerinck and van Delden 1902, effective name 1)
"Bacterium radiobacter" (Beijerinck and van Delden 1902) Lohnis 1905, effective name 1)
"Rhizobium radiobacter" (Beijerinck and van Delden 1902) Pribram 1933, effective name 1)
"Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934, effective name 1)
"Alcaligenes radiobacter" (Beijerinck and van Delden 1902) Conn 1939, effective name 1)
"Pseudomonas radiobacter" (Beijerinck and van Delden 1902) Krasil'nikov 1949, effective name 1) in [Krasil'nikov NA (1949)]
Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Zhang et al. 2014, emended name 2) in [Zhang L et al. (2014a), Skerman VBD et al. (1980)]
Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993 in [Sawada H et al. (1993)]
Rhizobium radiobacter (Beijerinck and van Delden 1902) Young et al. 2001 in [Young JM et al. (2001)]
type strain of "Rhizobium radiobacter": DSM:30147, CIP:104325, HAMBI:1814, ICMP:5785, IFO:13532, JCM:20371, BCCM/LMG:140, NCCB:27005, NCIMB:9042, NCPPB:3001, ATCC:19358, NBRC:13532
heterotypic synonym
Agrobacterium genomic group 4
heterotypic synonym
Agrobacterium genomosp. 4
heterotypic synonym
Agrobacterium genomovar 4
heterotypic synonym
Agrobacterium genomovar G4
Lineage( full )
cellular organisms; Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium; Agrobacterium tumefaciens complex
   Entrez records   
Database name Subtree links Direct links Links from type
Nucleotide 18,161 15,891 259
Protein 594,192 521,173 -
Structure 141 114 -
Genome 1 1 -
Popset 356 356 -
GEO Datasets 62 62 -
PubMed Central 26,961 26,961 -
Gene 51,210 32,364 -
SRA Experiments 285 282 -
Protein Clusters 5,639 5,639 -
Identical Protein Groups 325,911 306,826 -
Bio Project 138 117 -
Bio Sample 383 365 12
Bio Systems 765 503 -
Assembly 221 208 3
Probe 5 5 -
PubChem BioAssay 95 94 -
Taxonomy 22 1 -

Notes:

Comments and References:

Skerman VBD et al. (1980)
Skerman, V.B.D., McGowan, V., and Sneath, P.H.A. "Approved Lists of Bacterial Names." Intl. J. Syst. Bacteriol. (1980) 30(1):225-420.
Bergey DH et al. (1923)
Bergey, D.H., Harrison, F.C., Breed, R.S., Hammer B.W., and Huntoon, F.M. Bergey's Manual of Determinative Bacteriology, 1st ed. (1923) The Williams and Wilkins Co., Baltimore, pp. 1-442. [No PubMed record available.]
Krasil'nikov NA (1949)
Krasil'nikov, N.A.: Guide to the Bacteria and Actinomycetes [Opredelitelv Bakterii i Actinomicetov], (1949). Akad. Nauk SSSR, Moscow, pp. 1-830. [No PubMed record available.]
Zhang L et al. (2014a), PubMed: abstract
Zhang, L,, Li, X., Zhang, F., and Wang, G. "Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993." Stand Genomic Sci. (2014) 9:574-584.
Sawada H et al. (1993), PubMed: abstract
Sawada, H., Ieki, H., Oyaizu, H., and Matsumoto, S. "Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes." Int. J. Syst. Bacteriol. (1993) 43:694-702.
Young JM et al. (2001), PubMed: abstract
Young, J.M., Kuykendall, L.D., Martinez -Romero, E., Kerr, A., and Sawada, H. "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 Lajudieet al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis." Int. J. Syst. Evol. Microbiol. (2001) 51:89-103.
Agrobacterium tumefaciens = Agrobacterium radiobacter = Rhizobium radiobacter
Young et al. (2001) reclassify Agrobacterium tumefaciens as Rhizobium radiobacter, essentially for the reasons outlined by Sawada et al. (1993). The proposal was strongly opposed by other members of the scientific community (Farrand et al., 2003). The Judicial Commission (JUDICIAL OPINION 94) (2014) notes that Agrobacterium radiobacter has nomenclatural priority over A. tumefaciens when treated as heterotypic synonyms, but that Agrobacterium tumefaciens retains the status of type specie of the genus Agrobacterium. The binomen A. tumefaciens is presently given priority in the NCBI taxonomy database due to: a) its status as type species, and b) its far greater prevalence in the scientific literature.
Beijerinck MW & van Delden A (1902)
Beijerinck, M.W., and van Delden, A. "Uber die Assimilation des freien Stickstoffs durch Bakterien." Zentralbl. Bakteriol. Parasitenk. Infektionskr. Hyg. Abt. II (1902) 9:2-42. [No PubMed record available.]
Bergey 8
Buchanan, R.E., and Gibbons, N.E. (editors): Bergey's Manual of Determinative Bacteriology, 8th edition. The Williams and Wilkins Co., Balitmore, 1974. [Description] [No PubMed record available.]
Bergey DH et al. (1923)
Bergey, D.H., Harrison, F.C., Breed, R.S., Hammer B.W., and Huntoon, F.M. Bergey's Manual of Determinative Bacteriology, 1st ed. (1923) The Williams and Wilkins Co., Baltimore, pp. 1-442. [No PubMed record available.]
Bergey DH et al. (1934)
Bergey, D.H., Breed, R.S., Hammer B.W., Huntoon, F.M., Murray, E.G.D., and Harrison, F.C. Bergey's Manual of Determinative Bacteriology, 4th ed. (1934) The Williams and Wilkins Co., Baltimore, pp. 1-664. [No PubMed record available.]
Bouzar H (1994)
Bouzar, H. "Request for a Judicial Opinion concerning the type species of Agrobacterium." Int. J. Syst. Bacteriol. (1994) 44:373-374. [No PubMed record available.]
Conn HJ (1939)
Conn, H.J. "Genus III. Alcaligenes Castellani and Chalmers." In: Bergey, Breed, Murray, and Hitchens (eds.), Bergey's Manual of Determinative Bacteriology, 5th ed. (1939) The Williams and Wilkins Co., Baltimore. pp. 95-102. [No PubMed record available.]
Conn HJ (1942), other link:http://jb.asm.org/cgi/reprint/44/3/353?view=long&pmid=16560572
Conn, H.J. "Validity of the genus Alcaligenes." J. Bacteriol. (1942) 44:353-360. [No abstract available.]
Farrand SK et al. (2003)
Farrand, S.K., van Berkum, P.B., and Oger, P. "Agrobacterium is a definable genus of the family Rhizobiaceae." Int. J. Syst. Evol. Microbiol. (2003) 53:1681-1687. Published online 13 December 2002: DOI 10.1099/ijs.0.02445-0 [Note: cosigned by 83 others in addition to the three principal authors.]
Garrity GM et al. (2011)
Garrity, G.M., Labeda, D.P., and Oren, A. "Judicial Commission of the International Committee on Systematics of Prokaryotes. XIIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 3, 4 and 6 August 2008, Istanbul, Turkey." Int. J. Syst. Evol. Microbiol. (2011) 61:2775-2780.
Gaunt MW et al. (2001)
Gaunt, M.W., Turner, S.L., Rigottier-Gois, L., Lloyd-Macgilp, S.A., and Young, J.P. "Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia." Int. J. Syst. Evol. Microbiol. (2001) 51:2037-2048.
Judicial Commission (1995) (Agrobacterium tumefaciens)
Judicial Commission "Minutes of the Meetings, 2 and 6 July 1994, Prague, Czech Republic." Int. J. Syst. Bacteriol. (1995) 45:195-196. (Note: the Judicial Commission rejects the proposal of Sawada et al. (1993) and retains Agrobacterium tumefaciens [Minute 18].) [No PubMed record available.]
Krasil'nikov NA (1949)
Krasil'nikov, N.A.: Guide to the Bacteria and Actinomycetes [Opredelitelv Bakterii i Actinomicetov], (1949). Akad. Nauk SSSR, Moscow, pp. 1-830. [No PubMed record available.]
Lieske R (1928)
Lieske, R. "Untersuchungen uber die Krebskrankheit bei Pflanzen, Tieren und Menschen." Zentralbl. Bakteriol. Parasitenk. Infektionskr. Hyg. Abt. I Orig. (1928) 108:118-146. [No PubMed record available.]
List of Changes in Taxonomic Opinion No. 21 (2015)
"Notification of changes in taxonomic opinion previously published outside the IJSEM." Int. J. Syst. Evol. Microbiol. (2015) 65:7-10.
Lohnis F (1905)
Lohnis, F. "Beitrage zur Kenntnis der Stickstoffbacterion." Zentralbl. Bakteriol. Parasitenk. Infektionskr. Hyg. Abt. II (1905) 14:87-101;582-604. [No PubMed record available.]
Mougel C et al. (2002)
Mougel, C., Thioulouse, J., Perriere, G., and Nesme, X. "A mathematical method for determining genome divergence and species delineation using AFLP." Int. J. Syst. Evol. Microbiol. (2002) 52:573-586. [N.B.: source of 'Agrobacterium genomic group' nomenclature]
Pribram E (1933)
Pribram, E.: Klassification der Schizomyceten. F. Deuticke, Leipzig, (1933) pp. 1-143. [No PubMed record available.]
Sawada H et al. (1993)
Sawada, H., Ieki, H., Oyaizu, H., and Matsumoto, S. "Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes." Int. J. Syst. Bacteriol. (1993) 43:694-702.
Smith EF & Townsend CO (1907)
Smith, E.F., and Townsend, C.O. "A plant-tumor of bacterial origin." Science (Washington) (1907) 25:671-673. [No PubMed record available.]
Velázquez E et al. (2020), doi:10.1099/ijsem.0.004443
Velázquez, E., Flores-Félix, J.D., Sánchez-Juanes, F., Igual, J.M., and Peix, Á. "Strain ATCC 4720T is the authentic type strain of Agrobacterium tumefaciens, which is not a later heterotypic synonym of Agrobacterium radiobacter." Int. J. Syst. Evol. Microbiol. (2020) 70(9):5172-5176.
Tindall BJ [JUDICIAL OPINION 94] (2014)
Tindall, B.J. "Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 has priority over Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 when the two are treated as members of the same species based on the principle of priority and Rule 23a, Note 1 as applied to the corresponding specific epithets. Opinion 94. Judicial Commission of the International Committee on Systematics of Prokaryotes." Int. J. Syst. Evol. Microbiol. (2014) 64:3590-3592.
Young JM et al. (1996) (reference with type strain information)
Young, J.M., Saddler, G.S., Takikawa, Y., De Boer, S.H., Vauterin, L., Gardan, L., Gvozdyak, R.I., and Stead, D.E. "Names of plant pathogenic bacteria 1864-1995." Rev. Plant Pathol. (1996) 75:721-763. [No PubMed record available.]
Young JM et al. (2001)
Young, J.M., Kuykendall, L.D., Martinez -Romero, E., Kerr, A., and Sawada, H. "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 Lajudieet al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis." Int. J. Syst. Evol. Microbiol. (2001) 51:89-103.
Young JM et al. (2006)
Young, J.M., Pennycook, S.R., and Watson, D.R.W. "Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an Opinion." Int. J. Syst. Evol. Microbiol. (2006) 56:491-493. Published online 25 November 2005. doi:10.1099/ijs.0.64030-0
Zhang L et al. (2014)
Zhang, L,, Li, X., Zhang, F., and Wang, G. "Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993." Stand. Genomic Sci. (2014) 9:574-584.

External Information Resources (NCBI LinkOut)

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Agrobacterium radiobacter meta-databases BacDive
8 records from this provider organism-specific BioCyc
Rhizobium radiobacter (Beijerinck and van Delden 1902) Young et al. 2001 taxonomy/phylogenetic Encyclopedia of life
11 records from this provider organism-specific Genomes On Line Database
Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
Agrobacterium tumefaciens culture/stock collections Global Catalogue of Microorganisms
Related Immune Epitope Information gene/protein/disease-specific Immune Epitope Database and Analysis Resource
67 records from this provider organism-specific Integrated Microbial Genomes
Alcaligenes radiobacter taxonomy/phylogenetic Integrated Taxonomic Information System
3 records from this provider taxonomy/phylogenetic Systematic Mycology and Microbiology Laboratory, Fungal Databases
Wikipedia taxonomy/phylogenetic iPhylo
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Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.

Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. PubMed: 32761142 PMC: PMC7408187.


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