Taxonomy browser (Agrobacterium radiobacter)

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Taxonomy browser (Agrobacterium radiobacter)

Agrobacterium radiobacter

Taxonomy ID: 362 (for references in articles please use NCBI:txid362)

current name

Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) in [Skerman VBD et al. (1980)]

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, personal::EX 3.24.2, KCTC :22091, KACC:10798, CECT:4112, BCRC :10372

basionym:

"Bacillus radiobacter" Beijerinck and van Delden 1902, effective name

homotypic synonym:

Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993, emended name in [Sawada H et al. (1993)]

Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Zhang et al. 2014, emended name in [Zhang L et al. (2014a)]

vernacular name:

Agrobacterium genomosp. 4

equivalent:

Agrobacterium genomic group 4

Agrobacterium genomovar 4

Agrobacterium genomovar G4

homotypic synonym:

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

"Rhizobium radiobacter" (Beijerinck and van Delden 1902) Pribram 1933, effective name²⁾

"Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934, effective name³⁾

"Alcaligenes radiobacter" (Beijerinck and van Delden 1902) Conn 1939, effective name⁴⁾

"Pseudomonas radiobacter" (Beijerinck and van Delden 1902) Krasil'nikov 1949, effective name⁵⁾ in [Krasil'nikov NA (1949)]

Rhizobium radiobacter (Beijerinck and van Delden 1902) Young et al. 2001 in [Young JM et al. (2001)]

includes:

Agrobacterium sp. NCIB 9042

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 (Approved Lists 1980) in [Skerman VBD et al. (1980)]

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

includes:

Agrobacterium sp. UQM 1685

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	1,892	1,240	990
Protein	44,152	37,318	-
Genome	1	1	-
Popset	89	89	-
PubMed Central	1,359	1,359	-
Gene	10,526	5,255	-
SRA Experiments	10	5	-
Identical Protein Groups	33,132	29,213	-
BioProject	12	7	-
BioSample	19	11	8
Assembly	26	24	-
Taxonomy	2	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) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).
3) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).
4) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).
5) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).

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.

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.

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.

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.]

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 species of the genus Agrobacterium.

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. (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.]

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.]

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.]

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.]

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]

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.

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.

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.

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.

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.

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.

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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

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