Numerical Taxonomic Analysis of Agrobacterium

Kersters, Karel; Ley, J. De; Sneath, P. H. A.; Sackin, M. J.

doi:10.1099/00221287-78-2-227

Cited by 138 publications

(47 citation statements)

References 24 publications

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“…The most striking conclusion is the excellent agreement between the present data and the division of the agrobacteria into clusters and groups, on the basis of phenotypic and genotypic criteria (De Ley, 1972;Kersters et al 1973). The strains with a hybrid-T,(,, around 75 "C belong in the same group or cluster as the reference strain.…”

Section: Discussionsupporting

confidence: 59%

“…The strains used are listed in Table I ; many of them are briefly described elsewhere (Kersters et al 1973). As controls we included Salmonella typhimurium I and Acetobacter aceti ch31, which have a very low relationship with the agrobacteria (5.…”

Section: D E Ley R Tijtgat J D E Smedt a N D M Michiels M E T mentioning

confidence: 99%

“…(1973 As reference strains for hybridization we selected a representative of each of the three major Agrobacterium groups: Agrobacterium tumefaciens s6 and TTI I I from the groups of the same name in cluster I and A . rhizogenes T R~ from cluster 2 (De Ley, 1972;Kersters et al 1973). In most cases only the stable duplex was allowed to form, by hybridization at 59 "C, followed by denaturing the hybrid.…”

Section: J D E Ley R Tijtgat J D E Smedt a N D M M I C H I E L Smentioning

confidence: 99%

“…'Low ' refers to a weakly stable molecular hybrid with Tflt(e) < 62 "C. The division into clusters and groups was made according to De Ley (1972) and Kersters et a/. (1973 As reference strains for hybridization we selected a representative of each of the three major Agrobacterium groups: Agrobacterium tumefaciens s6 and TTI I I from the groups of the same name in cluster I and A .…”

Section: J D E Ley R Tijtgat J D E Smedt a N D M M I C H I E L Smentioning

confidence: 99%

“…tumefaciens strains), the 'rubi' group and two very small groups hybridize at about 10 to 15 %. Within cluster I the DNA of the seven groups hybridize at about 50 % and within each group at least 80 % (De Ley, 1972;Kersters, De Ley, Sneath & Sackin, 1973;5. De Ley, A. Reynaerts & H. Cattoir, unpublished).…”

Section: Introductionmentioning

confidence: 99%

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Thermal Stability of DNA: DNA Hybrids within the Genus Agrobacterium

Ley

Tijtgat

Smedt

et al. 1973

Journal of General Microbiology

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S U M M A R YMolecular hybrids were prepared between unlabelled DNA from representative strains of eleven genetic races of Agrobacterium and [I4C]DNA from typical strains of each of the three main races. The thermal stability of each hybrid was determined. The nature of the hybrids formed varied with the incubation temperature and the kind of DNA used. Hybridization in 2 x SSC-30 % dimethylsulphoxide below 59 "C yielded two kinds of hybrids: a labile one of unknown nature, denaturing below 59 "C, and a more or less stable hybrid denaturing above that temperature. The latter was the only one formed in hybridizations at or above 59 "C. There were three kinds of stable hybrids. Within each of the main Agrobacterium races thermal stability of the molecular hybrid was about the same (within 2 "C) as for the homoduplex. Between two races of 50 % DNA relatedness, the duplexes were about 6 "C less stable. Between races of 10 to I 5 % DNA relatedness, the duplexes were weak, and the stability was at least 13 "C lower. The stability of the hybrids decreased concomitantly with the degree of DNA relatedness. The decreased hybrid denaturation curve is not due to AT-rich sequences. The less two races of agrobacteria appeared to be evolutionarily related, the more mutations occurred within the common part. I N T R O D U C T I O NFrom previous studies it appeared that the genus Agrobacterium is genetically very heterogeneous. DNA of cluster I (typical Agrobacterium tumefaciens and A. radiobacter strains), cluster 2 ( A . rhizogenes and atypical A . tumefaciens strains), the 'rubi' group and two very small groups hybridize at about 10 to 15 %. Within cluster I the DNA of the seven groups hybridize at about 50 % and within each group at least 80 % ( Mutational events modified considerable parts of the genomes, preventing in vitro molecular hybridization. Considering the evolutionary history of a bacterial genus, one can wonder whether mutations also occurred within the common DNA parts. For an experimental answer to that question we prepared a number of DNA-hybrids between the genomes of different Agrobacterium groups and clusters, and determined their thermal stability which is interpreted as a measure of base-pairing imperfections, and mutational differences (Brenner & Cowie, 1967). We established that decreased hybrid denaturation curves were not due to preferential binding of heterologous AT-rich DNA sequences.

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Section: Discussionsupporting

confidence: 59%

Section: D E Ley R Tijtgat J D E Smedt a N D M Michiels M E T mentioning

confidence: 99%

Section: J D E Ley R Tijtgat J D E Smedt a N D M M I C H I E L Smentioning

confidence: 99%

Section: J D E Ley R Tijtgat J D E Smedt a N D M M I C H I E L Smentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Thermal Stability of DNA: DNA Hybrids within the Genus Agrobacterium

Ley

Tijtgat

Smedt

et al. 1973

Journal of General Microbiology

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Agrobacterium

Young¹,

Kerr²,

Sawada³

2015

Bergey's Manual of Systematics of Archaea and Bacteria

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A.gro.bac.te' ri.um . Gr. n. agros a field; Gr. dim. neut. n. bakterion a small rod; M.L. neut. n. Agrobacterium a small field rod. Proteobacteria / Alphaproteobacteria / Rhizobiales / Rhizobiaceae / Agrobacterium Rods 0.6–1.0 × 1.5–3.0 μm , occurring singly or in pairs. Nonsporeforming. Gram negative. Motile by 1–4 peritrichous flagella. Aerobic , possessing a strictly respiratory type of metabolism with oxygen as the terminal electron acceptor. Some strains are capable of anaerobic respiration in the presence of nitrate. Most strains are able to grow under reduced oxygen tensions in plant tissues. Optimal temperature for growth: 25–28°C. Colonies are usually convex, circular, smooth, nonpigmented to light beige. Growth on carbohydrate‐containing media is usually accompanied by copious extracellular polysaccharide slime . Catalase positive. Usually oxidase positive and urease positive. Indole is not produced. Chemoorganotrophs, utilizing a wide range of carbohydrates, salts of organic acids, and amino acids as carbon sources, but not cellulose, starch, agar, or chitin. Produce an acid reaction in mineral salts media containing mannitol and other carbohydrates . Ammonium salts and nitrates can serve as nitrogen sources for strains of some species; others require amino acids and additional growth factors. 3‐ketoglycosides are produced by the majority of strains belonging to A . tumefaciens . Strains of some species in this genus invade the crown, roots, and stems of a great variety of dicotyledonous and some gymnospermous plants via wounds, causing transformation of the plant cells into autonomously proliferating tumor cells . Oncogenicity is correlated with the presence of a large tumor‐inducing plasmid. Habitat: soil. Oncogenic strains occur mainly in soils previously contaminated with diseased plant material. Some non‐oncogenic Agrobacterium strains have been isolated from human clinical specimens. The mol % G + C of the DNA is : 57–63. Type species : Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942, 359 AL ( Bacterium tumefaciens Smith and Townsend 1907, 672; Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942, 359; Agrobacterium radiobacter biovar radiobacter (Beijerinck and van Delden 1902) Keane, Kerr and New 1970, 594; Agrobacterium radiobacter biovar tumefaciens (Smith and Townsend 1907) Keane, Kerr and New 1970, 594; Agrobacterium radiobacter pathovar tumefaciens (Smith and Townsend 1907) Young, Dye, Bradbury, Panagopoulos and Robbs 1978, 156.)

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Rhizobium

Kuykendall¹,

Young²,

Martı́nez-Romero³

et al. 2015

Bergey's Manual of Systematics of Archaea and Bacteria

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Rhi.zo' bi.um . Gr. n. rhiza a root; Gr. n. bios life; M.L. neut. n. Rhizobium that which lives in a root. Proteobacteria / Alphaproteobacteria / Rhizobiales / Rhizobiaceae / Rhizobium Rods 0 . 5–1 . 0 × 1 . 2–3 . 0 µm . Nonsporeforming. Gram negative. Motile by 1–6 peritrichous flagella . Fimbriae have been described on some strains. Aerobic , possessing a respiratory type of metabolism with oxygen as the terminal electron acceptor. Optimal temperature for growth, 25–30°C; some species can grow at temperatures >40°C. Optimal pH for growth, 6–7; range pH 4–10. Generation times of Rhizobium strains are 1.5–5.0 h. Colonies are usually white or beige, circular, convex, semi‐translucent or opaque, raised and mucilaginous, usually 2–4 mm in diameter within 3–5 days on yeast‐mannitol‐mineral salts agar ( YMA ). Growth on carbohydrate media is usually accompanied by copious amounts of extracellular polysaccharide . Pronounced turbidity develops after 2 or 3 days in aerated or agitated broth. Chemoorganotrophic, utilizing a wide range of carbohydrates and salts of organic acids as sole carbon sources, without gas formation. Cellulose and starch are not utilized. Produce an acidic reaction in mineral‐salts medium containing mannitol or other carbohydrates . Ammonium salts, nitrate, nitrite, and most amino acids can serve as nitrogen sources. Strains of some species will grow in a simple mineral salts medium with vitamin‐free casein hydrolysate as the sole source of both carbon and nitrogen, but strains of many species require one or more growth factors such as biotin, pantothenate, or nicotinic acid. Peptone is poorly utilized. Casein, starch, chitin, and agar are not hydrolyzed. All known Rhizobium species include strains which induce hypertrophisms in plants as root nodules with or without symbiotic nitrogen fixation . Some cells of symbiotic bacterial species enter root hair cells of leguminous plants (Family Leguminosae) via invagination or by wounds (“crack entry”) and elicit the production of root nodules wherein the bacteria engage as intracellular symbionts, usually fixing nitrogen. Many well‐defined nodulation ( nod ) and nitrogen fixation ( nif ) genes are clustered on large plasmids or megaplasmids (pSyms). Plasmid transfer between species results in the expression and stable inheritance of the particular plant‐interactive properties of the plasmid‐donor species. Plant host specificity is usually for a few legume genera but may, in some strains, include a wide variety of legume genera and is to some extent determined by the chemical structure of the lipochito‐oligosaccharide Nod factors produced. These chitin‐like molecules induce nodule organogenesis in the absence of bacteria. In root nodules the bacteria occur as endophytes that exhibit pleomorphic forms , termed “ bacteroids ”, which reduce or fix gaseous atmospheric nitrogen into a combined form utilizable by the host plant . The mol % G + C of the DNA is : 57–66. Type species : Rhizobium leguminosarum (Frank 1879) Frank 1889, 338 ( Schinzia leguminosarum Frank 1879, 397.)

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Numerical Taxonomic Analysis of Agrobacterium

Cited by 138 publications

References 24 publications

Thermal Stability of DNA: DNA Hybrids within the Genus Agrobacterium

Thermal Stability of DNA: DNA Hybrids within the Genus Agrobacterium

Agrobacterium

Rhizobium

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