A Common Origin pf Rickettsiae and Certain Plant Pathogens

Weisburg, William G.; Woese, Carl R.; Dobson, Michael E.; Weiss, Emilio

doi:10.1126/science.3931222

Cited by 80 publications

(58 citation statements)

References 19 publications

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“…To clarify the phylogenetic relationships of the species belonging to the genera Sphingomonas and Rhizomonas and Erythrobacter longus, we determined the 16s rRNA sequence of Rhizomonas suberifaciens I F 0 1521 lT (Fig. 1) and compared it with the sequences of eight species belonging to the genus Sphingomonas (29), the sequences of the bacteriochlorophyll-containing bacteria Porphyrobacter neustonensis (4) and Roseobacter denitriJicans (22), and the sequences of 30 other species belonging to the alpha subclass (30,40), Magnetospirillum magnetotacticum (2), and Rhodospirillum rubrum (30,40); alpha-2 group species Hyphomicrobium vulgare (25), Rhodomicrobium vanniefii (40), Ancyfobacter aquaticus (39), Afipia felis (37), Blastobacter denitrificans (37), Bradyrhizobium japonicum (37), Methylosinus trichosporium (30), Methylobacterium organophilum (30), Agrobacterium tumefaciens (30,40), Bartonella bacilliformis (18), Rochalimaea quintana (36), Caulobacter bacteroides (27), and Pseudomonas diminuta (30); alpha-3 group species Hyphomonas jannaschiana (25), Hirschia baltica (21), Paracoccus denitr$cans (15,40), Rhodobacter capsufatus (30,40), and Roseobacter denitrificans (4); alpha4 group species Erythrobacter longus (40) and Porphyrobacter neustonensis (4); alpha group species Cowdria ruminantium (3), Ehrlichia risticii (34,35), Rickettsia prowazekii (35), and Wolbachia pipientis (16); delta-3 group species Escherichia coli (30). Bar = 0.01 K,,, unit.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

Takeuchi

Sawada

Oyaizu

et al. 1994

International Journal of Systematic Bacteriology

101

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Ministq of Agriculture, Forestry and Fisheries, Akitsu, and Faculty of To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16s rFWA sequence of Rhizornonas suberifaciens I F 0 15211T (T = type strain) was determined. A phylogenetic analysis of aligned 16s rRNA gene sequences revealed that eight species of the genus Sphingomonas and R. suberifaciens are closely related to Erythrobacter longus and Porphyrobucter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonus species and R. suberifaciens are phylogenetically interrelated and comprise several subgroups. Our findings show that the genus and species definitions of these --organisms are in need of revision. Yabuuchi et al. (42). Sphingomonas macrogoltabidus and Sphingomonas terrae are polyethylene glycolutilizing bacteria (11, 12) which were previously classified as Flavobacterium species. Polyethylene glycol 4000 is utilized by a single bacterium, Sphingomonas terrae, but polyethylene glycol 6000 is utilized by symbiotic mixed cultures of two strains (13), and the dominant bacterium in the mixed cultures is Sphingomonas macrogoltabidus.Recently, we compared the 16s rRNA sequences of the eight previously described and newly proposed species of the genus Sphingomonas with the 16s rRNA sequences of 15 representative species belonging to the alpha subclass of the Proteobacteria (29), and we found that the eight Sphingomonas species form a large and heterogeneous cluster which is clearly separate from all other representatives of the alpha subclass of the Proteobacteria (26,38) except Erythrobacter longus (23,24).On the other hand, the genus Rhizomonas and the single species Rhizomonas suberifaciens were proposed by van Bruggen et al. (32) for the gram-negative, motile, rod-shaped bacteria that cause corky root of lettuce. Most strains of Rhizomonas suberifaciens are oligotrophic (31), but the morphological, physiological, and chemotaxonomic characteristics * Corresponding author. Mailing address: Institute for Fermentation, Osaka, 17-85, Juso-honmachi 2-chome7 Yodogawa-ku, Osaka 532, Japan. Phone: 06-300-6555. Fax: 06-300-6814. of these organisms are similar to those reported for Sphingomonas paucimobilis (33,42). Neither Rhizomonas suberifaciens nor Sphingomonas paucimobilis produces acid on peptone-glucose medium, but both organisms produce acid on ammonium or nitrate-glucose medium (6). Strains of these two species have the same isoprenoid quinone (ubiquinone 10) and similar fatty acid compositions (8, 17,33), and the results of grouping based on these two characteristics have been shown to coincide with the results of grouping based on rRNA-DNA homology data (33).On the basis of these findings, we suggested previously that species belonging to the genera Sphingomonas and Rhizomonus are closely related to each other (29).Recently, on the basis of sequencing data for 270 bases of 16s rRNA genes from eight strains of Rhizomonas species and eight strains of Sphing...

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Section: Resultsmentioning

confidence: 99%

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

Takeuchi

Sawada

Oyaizu

et al. 1994

International Journal of Systematic Bacteriology

101

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“…A similarity matrix was constructed with other eubacterial sequences by using a data base that included approximately 400 partial (oligonucleotide) 16s rRNA sequences from bacteria (11, 48; C. R. Woese, personal communication). Sequences from the following bacteria were selected, each representative of a major phylogenetic group: Agrobacterium tumefaciens (alpha subdivision of purple bacteria) (42,47), Pseudomonas testosteroni (beta subdivision of purple bacteria) (31, 49), Chromatium vinosum and Legionella pneumophila (gamma subdivision of purple bacteria) (48; C. R. Woese, personal communication), Desulfovibrio desulfuricans (delta subdivision of purple bacteria) (48; C. R. Woese, personal communication), and Bacillus subtilis (gram positive) (12). Sequences were decomposed into RNase T1 oligonucleotides, stretches of bases that contain no guanosine but end in a single G. These were compared by signature analysis with existing T1 oligonucleotide catalogs available for various bacteria including Xanthomonas maltophilia and X .…”

Section: Methodsmentioning

confidence: 99%

Xylella fastidiosa gen. nov., sp. nov: Gram-Negative, Xylem-Limited, Fastidious Plant Bacteria Related to Xanthomonas spp.

Wells

Raju

Hung

et al. 1987

International Journal of Systematic Bacteriology

542

308

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Twenty-five phenotypically and genotypically similar strains of a fastidious, xylem-limited bacterium were isolated from 10 plant disease sources including Pierce's disease of grapevines, phony disease of peach, periwinkle wilt, and leaf scorches of almond, plum, elm, sycamore, oak, and mulberry. The cells were single (occasionally filamentous), nonmotile, aflagellate straight rods (0.25 to 0.35 by 0.9 to 3.5 pm). They were gram negative, catalase positive, and oxidase negative, utilized hippurate, and produced gelatinase and often beta-lactamase but not beta-galactosidase, coagulase, lipase, amylase, phosphatase, indole, or HZS. The bacteria were strict aerobes with optimum growth at 26 to 28°C and pH 6.5 to 6.9 and had doubling times of 0.45 to 1.98 days in periwinkle wilt broth. Monoclonal antibodies prepared against the Pierce's disease bacterium reacted with all strains. DNA composition was 51 to 53 mol% guanine plus cytosine, and strains were at least 85% related in DNA hybridization. Sequencing of 16s ribosomal ribonucleic acid related them to the xanthomonads. These bacteria form a distinct group, and the name XyZeZZa fastidiosa is proposed, establishing a new genus with one species in the gamma subgroup of the eubacteria. Strain PCE-RR (ATCC 35879) is designated as the type strain. (13,16,26,27,33,36,37,41,44,45; J. Sherald, unpublished data).

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Section: Introductionmentioning

confidence: 99%

“…Methylobacterium nodulans ' is the name suggested for a recently discovered fourth group of root-nodule bacteria that are methylotrophic and closely related to known Methylobacterium species (Sy et al, 2001). The other rhizobia, known collectively as the fast-growers, are more closely related, but their clade in the SSU phylogeny (Maidak et al, 2000) also includes Agrobacterium ( plant gall-formers), Phyllobacterium (leaf and rhizosphere colonists), Mycoplana (branching soil bacteria), Brevundimonas bullata (formerly Mycoplana bullata, see Abraham et al, 1999) and possibly the animal pathogens Bartonella and Brucella (Moreno et al., 1990 ;Weisburg et al, 1985 ;Young et al, 1991).There has been controversy over the relationship between Agrobacterium and Rhizobium, which have long been recognized as close relatives (Fred et al, 1932). Some authors suggested that Agrobacterium should be subsumed into Rhizobium (de Ley, 1968 ; Graham, 1964 Graham, , 1976 Heberlein et al, 1967 ; Kerr, 1992 ;Sawada et al, 1993 ;White, 1972), but the splitting of Sinorhizobium and Mesorhizobium from Rhizobium weakened the case for such an amalgamation because it was not clear whether Agrobacterium formed a monophyletic clade with Rhizobium sensu stricto.…”

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confidence: 99%

Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia.

Gaunt¹,

Turner²,

Rigottier-Gois³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

372

204

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The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the α-Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination. Rhizobium, Sinorhizobium, Mesorhizobium, recA, atpD Keywords : INTRODUCTIONThe rhizobia are root-nodulating bacteria responsible for a significant part of the global fixation of nitrogen. The ability of rhizobia to nodulate plants and reduce N # is conferred by genes that are plasmid-borne in many species (Pueppke, 1996), and the lateral transfer The atpD and recA sequences and details of the SimPlot analyses are available as supplementary material in IJSEM Online (http :// ijs.sgmjournals.org/ ).Abbreviations : HKY85, Hasegawa-Kishino-Yano model ; K2P, Kimura's two-parameter model ; SSU, small subunit rRNA.The EMBL accession numbers for the sequences reported in this study are AJ294386-AJ294409 (atpD) and AJ294363-AJ294385 (recA). of these genes is the most likely explanation for their occurrence within several distinct clades of subgroup 2 of the α-Proteobacteria (Dobert et al., 1994 ; Kaijalainen & Lindstro$ m, 1989 ;Lindstro$ m et al., 1995 ;Young, 1998 ;Young & Johnston, 1989). The phylogeny of the nodulation genes is quite different from that of the small subunit rRNA (SSU or 16S rRNA) genes in these bacteria. As in other bacterial groups, the SSU phylogeny has had a major influence on our current perception of evolutionary relationships among rhizobia ( Willems & Collins, 1993 ;Young, 1996 ;Young et al., 1991). More than 20 species have been described, and they are classified into the genera Rhizobium, Sinorhizobium, Allorhizobium, Mesorhizobium, Bradyrhizobium and Azorhizobium as well as ' Methylobacterium nodulans ' (de Lajudie et al., 1994' (de Lajudie et al., , 1998b Dreyfus et al., 1988 ; Jarvis et al., 1997 ; Jordan, 1982 ;Sy et al., 2001 M. W. Gaunt and others ing much slower growth on laboratory media (Dreyfus et al., 1988 ; Fred et al., 1932 ; Jordan, 1982). They are also fairly distant in the SSU p...

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A Common Origin pf Rickettsiae and Certain Plant Pathogens

Cited by 80 publications

References 19 publications

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

Xylella fastidiosa gen. nov., sp. nov: Gram-Negative, Xylem-Limited, Fastidious Plant Bacteria Related to Xanthomonas spp.

Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia.

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