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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:4720, CCM:1000, CCUG:3555, CFBP:2412, CIP:104335, DSM:30150, ICMP:5793, BCCM/LMG:182, NCIMB:8150, NCPPB:2992, IAM:14141, IAM:1524, JCM:21034, personal::A1
not considered type of Agrobacterium tumefaciens: ATCC:23308, CFBP:2413, HAMBI:1811, ICMP:5856, BCCM/LMG:187, NCPPB:2437, DSM:30205, personal::B6, IAM:13129
basionym:
"Bacterium tumefaciens" Smith and Townsend 1907, effective name
homotypic synonym:
"Pseudomonas tumefaciens" (Smith and Townsend 1907) Duggar 1909, effective name 1)
"Phytomonas tumefaciens" (Smith and Townsend 1907) Bergey et al. 1923, effective name 2) in [Bergey DH et al. (1923)]
"Polymonas tumefaciens" (Smith and Townsend 1907) Lieske 1928, effective name 3)
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
vernacular name:
Agrobacterium genomosp. 1
equivalent:
Agrobacterium genomic group 1
Agrobacterium genomic species 1
Agrobacterium genomic species G1
Agrobacterium tumefaciens genomovar G1
NCBI BLAST name: a-proteobacteria
Rank: species
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
heterotypic synonym
Agrobacterium fabacearum Delamuta et al 2020 in [Delamuta JRM et al. (2020)]
type strain of Agrobacterium fabacearum: personal::CNPSo 675, UMR:1457, BCCM/LMG:31642, personal::CHIMBORAZO pallatanga 1 Ch2
includes:
Agrobacterium sp. CNPSo 675
Agrobacterium sp. H13-3
Rhizobium sp. CNPSO675
equivalent:
Rhizobium lupini H13-3
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 19,460 17,781 314
Protein 745,508 673,070 -
Structure 154 136 -
Genome 1 1 -
Popset 320 320 -
GEO Datasets 135 135 -
PubMed Central 33,216 33,216 -
Gene 51,385 38,001 -
SRA Experiments 449 448 -
Protein Clusters 5,639 5,639 -
Identical Protein Groups 365,586 347,761 -
BioProject 179 154 -
BioSample 573 556 2
Assembly 284 266 -
PubChem BioAssay 99 99 -
Taxonomy 25 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.]
Delamuta JRM et al. (2020), PubMed: abstract
Delamuta,. J.R.M., Scherer, A.J., Ribeiro, R.A., and Hungria, M. "Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov." Int. J. Syst. Evol. Microbiol. (2020) 70(7):4233-4244.
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.]
Wibberg D et al. (2011)
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Sczcepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Puhler, A., and Schluter, A. "Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid." J. Biotechnol. (2011) 155:50-62.
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.]
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.
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]
JUDICIAL OPINION 127 (2022), doi:10.1099/ijsem.0.005708
Arahal, D.R., Bull, C.T., Busse, H.-J., Christensen, H., Chuvochina, M., Dedysh, S.N., Fournier, P.-E., Konstantinidis, K.T., Parker, C.T., Rossello-Mora, R., Ventosa, A., and Göker M. "Judicial Opinions 123-127." Int. J. Syst. Evol. Microbiol. (2022) 72(12):005708. [N.B.: Judicial Opinion 127 assigns the strain ATCC 4720 as the type strain of Agrobacterium tumefaciens.]
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.
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.]
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.]
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.
Huang YY et al. (2015), other link:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457062/
Huang, Y.-Y., Cho, S.-T., Lo, W.-S., Wang, Y.-C., Lai, E.-M., and Kuo, C.-H. "Complete genome sequence of Agrobacterium tumefaciens Ach5." Genome Announc. 3(3):e00570-15.
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.]
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. (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
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.]
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.
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
16 records from this provider organism-specific BioCyc
Rhizobium radiobacter (Beijerinck and van Delden 1902) Young et al. 2001 taxonomy/phylogenetic Encyclopedia of life
GOLD: 62 Organisms 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
92 records from this provider organism-specific Integrated Microbial Genomes
Alcaligenes radiobacter taxonomy/phylogenetic Integrated Taxonomic Information System
Agrobacterium tumefaciens | SeqCode Registry taxonomy/phylogenetic SeqCode Registry
3 records from this provider taxonomy/phylogenetic Systematic Mycology and Microbiology Laboratory, Fungal Databases
Agrobacterium tumefaciens Smith & Townsend, 1907 taxonomy/phylogenetic World Register of Marine Species
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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