Intra- and Intergeneric Similarities of Ribosomal Ribonucleic Acid Cistrons of Free-Living, Nitrogen-Fixing Bacteria

Abstract

'*C-labeled ribosomal ribonucleic acid (rRNA) was prepared from Azoto bacter chroococcum NCIB 8002, Azotobacter paspali 8A, Azomonas agilis NCIB 8636, Azomonas insignis WR 30, Beuerinckia indica NCIB 8712, and Azospirillum brasilense ATCC 29145. These rRNA's were hybridized under stringent conditions with filter-fixed deoxyribonucleic acid from a great variety of gram-negative bacteria. Each hybrid was described by: (i) the temperature at which 50% of the hybrid was denatured, and (ii) the percent rRNA binding (amount in micrograms of rRNA duplexed to 100 pg of deoxyribonucleic acid). These data were used to construct rRNA similarity maps. The following conclusions could be drawn concerning rRNA cistron similarities. (i) Bacterial genera with free-living, aerobic, nitrogen-fixing members are very diverse and belong to different rRNA superfamilies. The present family Azotobacteriaceae is not a biological unit, and its status as a family is highly questionable. (ii) Azotobacter chroococcum, Azoto bacter vinelandii, Azoto bacter beijerinckii, Azoto bacter paspali, Azoto bacter miscellum, Azotobacter armeniae, and Azotobacter nigricans belong in the genus Azotobacter. Any synonymy of these names remains to be determined. Azomonas agilis, Azomonas insignis, and Azomonas macrocytogenes constitute independent branches, which are about equidistant from Azotobacter and section I of Pseudomonas as presented in Bergey 's Manual of Determinative Bacteriology, 8th ed. Xanthomonas, Alteromonas vaga, and Alteromonas communis are located in the same rRNA superfamily. (iii) The genus Beijerinckia appears to be rather heterogeneous. Its closest relatives appear to be Xantho bacter autotrophicus, "Mycobacterium" flavum, "Pseudomonas" azotocolligans, "Pseudomonas" diminuta, the authentic rhodopseudomonads, and some other organisms. These organisms belong in the same rRNA superfamily as Azospirillum, Agrobacterium, Rhizo bium, Aceto bacter, Glucono bacter, and Zymomonas. (iv) Derxia belongs in still another rRNA superfamily , together with Chromobacterium, Janthinobacterium, the Pseudomonas acidovorans and Pseudomonas solanacearum groups, Alcalienes, and a few other taxa. (v) The following organisms were generically misnamed: "Azomonas insignis" ATCC 12523, "Mycobacterium" flavum 301, "Pseudomonas" azotocolligans ATCC 12417, "Pseudomonas" diminuta CCEB 513, and "Rhodopseudomonas" gelatinosa (all strains examined).Molecular biological methods, such as deoxyribonucleic acid (DNA)-DNA or DNA-ribosomal ribonucleic acid (rRNA) hybridizations, which directly compare bacterial genomes, have opened new perspectives for bacterial classification. Many bacterial genera are phylogenetic d y too far removed from each other to form stable DNA-DNA hybrids. DNA-DNA hybridizations are useful either within a genus, such as Agrobacterium (ZO), or between genera which have not diverged too much, such as in the Enterobacteriaceae (12; D. Izard, C. Ferragut, and H. Leclerc, in press). rRNA's are conservative molecules (25, 36, 43). There is a good corre...

Genotypic Relationships and Taxonomic Localization of Unclassified Pseudomonas and Pseudomonas-Like Strains by Deoxyribonucleic Acid:Ribosomal Ribonucleic Acid Hybridizations

“…We pointed out previously (12,14) that the authentic genus Pseudomonas should be limited to the Pseudomonaspuorescens rRNA branch and that the members of the Azotobacteraceae as defined in Bergey 's Manual of Systematic Bacteriology (53) are the closest relatives of this group. The emended genus Pseudomonas consists of (i) all Pseudomonas species from section I in Bergey's Manual of Systematic Bacteriology (41) , (ii) previously unclassified plant-pathogenic species (15) , and (iii) the following strains examined in the present study (in decreasing order of relatedness to reference strain Pseudomonas puorescens LMG 1794T): "Pseudomonas septica" LMG 2290, Pseudomonas synxantha LMG 2190T, Pseudomonas taetrolens LMG 2336T, Pseudomonas stutzeri (formerly Pseudomonas per- Tm(e, % rRNA T,,(<,, % rRNA T,(,, % rRNA Tm(,, % rRNA Tm(e) % rRNA T+, % rRNA TmC,) % rRNA (Table 4).…”

Phylogenetic relationships of the helical-shaped bacteria in the .ALPHA. Proteobacteria inferred from 16S rDNA sequences.

“…The generic name Rhodospirillum (Molisch, 1907) was given for helical phototrophic bacteria. According to 165 rRNA oligonucleotide cataloging (Woese et al, 1984a, 1984b, 1985) and DNA-rRNA hybridization studies (De Smedt et al, 1980;Pot et al, 1989Pot et al, , 1992, Aquaspirillum and Oceanospirillum are very heterogeneous genera which spread over the Proteobacteria a, ~3, and y groups. Rhodospirillum and Azospirillum are placed in the Proteobacteria a group, but Rhodospirillum is a heterogeneous genus which has been supported by both physiological (Truper and Imhoff, 1989) and chemotaxonomic data (Imhoff, 1984;Kato et al, 1985).…”

Phylogenetic analyses of the nitrogen-fixing genus Derxia

“…The genus Derxia has been considered to have a relationship with the diazotrophic genera, Azotobacter, Azomonas, Beijerinckia, and Pseudomonas, based on morphological, physiological, and chemotaxonomic characteristics (Becking, 1984(Becking, , 1991; based on the method of rRNA cistron similarity, De Smedt et al (1980) have also grouped the genus Derxia with Janthinobacterium, Alcaligenes, and a few other taxa of bProteobacteria; the genus was, however, placed in the family Beijerinckiaceae (a-Proteobacteria) in the latest edition of "Bergey's Manual of Systematic Bacteriology" without any comments regarding this placement (Garrity and Holt, 2000). The phylogenetic position of Derxia has not previously been studied, making the taxonomy of Derxia a source of confusion.…”