Taxonomy browser (Agrobacterium tumefaciens)

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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, DSM :30205, personal::B6

basionym:

"Bacterium tumefaciens" Smith and Townsend 1907, effective name¹⁾

homotypic synonym:

"Pseudomonas tumefaciens" (Smith and Townsend 1907) Duggar 1909, effective name¹⁾

"Phytomonas tumefaciens" (Smith and Townsend 1907) Bergey et al. 1923, effective name¹⁾ in [Bergey DH et al. (1923)]

"Polymonas tumefaciens" (Smith and Townsend 1907) Lieske 1928, effective name¹⁾

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

Beijerinckia fluminensis Döbereiner and Ruschel 1958, nom. approb.²⁾ in [Skerman VBD et al. (1980)]

type strain of Beijerinckia fluminensis: CIP:106281, UQM:1685

includes:

Agrobacterium sp. UQM 1685

heterotypic synonym

Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980)

homotypic synonym:

"Bacillus radiobacter" Beijerinck and van Delden 1902, effective name¹⁾

"Bacterium radiobacter" (Beijerinck and van Delden 1902) Lohnis 1905, effective name¹⁾

"Rhizobium radiobacter" (Beijerinck and van Delden 1902) Pribram 1933, effective name¹⁾

"Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934, effective name¹⁾

"Alcaligenes radiobacter" (Beijerinck and van Delden 1902) Conn 1939, effective name¹⁾

"Pseudomonas radiobacter" (Beijerinck and van Delden 1902) Krasil'nikov 1949, effective name¹⁾ in [Krasil'nikov NA (1949)]

Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Zhang et al. 2014, emended name³⁾ 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 Agrobacterium 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, CCUG :3354, IAM:12048

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; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium; Agrobacterium tumefaciens complex

Entrez records
Database name	Subtree links	Direct links	Links from type
Nucleotide	18,836	16,127	251
Protein	701,696	637,428	-
Structure	135	119	-
Genome	1	1	-
Popset	372	372	-
GEO Datasets	124	124	-
PubMed Central	32,176	32,176	-
Gene	37,526	32,369	-
SRA Experiments	375	369	-
Protein Clusters	5,639	5,639	-
Identical Protein Groups	353,045	336,058	-
BioProject	157	135	-
BioSample	476	456	13
Assembly	275	259	3
PubChem BioAssay	98	97	-
Taxonomy	21	1	-

Notes:

1) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).
2) 'Nom. approb.' (= nomen approbatum, = approved name) refers to a name which is included in the Approved Lists of Bacterial Names.
3) emend. (emendavit): Used when the alteration of the diagnostic characters or of the circumscription of a taxon modifies the nature of the taxon.

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.

Bergey DH et al. (1923)

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.]

Dobereiner J & Ruschel AP (1958)

Dobereiner, J., and Ruschel, A.P. "Uma nova especie de Beijerinckia." Revista de Biologia (1958) 1:261-272. [No PubMed record available.]

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(1):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)

Oggerin M et al. (2009)

Oggerin, M., Arahal, D.R., Rubio, V., and Marin, I. "Identification of Beijerinckia fluminensis strains CIP 106281T and UQM 1685T as Rhizobium radiobacter strains, and proposal of Beijerinckia doebereinerae sp. nov. to accommodate Beijerinckia fluminensis LMG 2819." Int. J. Syst. Evol. Microbiol. (2009) 59:2323-2328.

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 species 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.

Oggerin M et al. (2011)

Oggerin, M., Rubio, V., Marin, I., and Arahal, D.R. "The status of the species Beijerinckia fluminensis Dobereiner and Ruschel 1958. Request for an Opinion." Int. J. Syst. Evol. Microbiol. (2011) 61:1757-1759.

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.

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.]

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 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)

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.]

External Information Resources (NCBI LinkOut)

LinkOut	Subject	LinkOut Provider
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
82 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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A list of our current non-bibliographic LinkOut providers can be found here.

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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.

Comments and questions to info@ncbi.nlm.nih.gov