The phylogenetic relationships among the species of the genus Pedomicrobium were studied by comparing their 16S rRNA sequences. The Pedomicrobium species form a coherent phylogenetic cluster within the genera of the hyphal budding bacteria in the α-Proteobacteria. The sequences of two strains of Pedomicrobium australicum were obtained from DNAs extracted from nonviable freeze-dried cells, which are the only source of material available, and were found to be almost identical (level of similarity, 99.9%). Overall, the Pedomicrobium species are closely related, with sequence similarities ranging from 96.2 to 99.9%. Pedomicrobium manganicum is phylogenetically the most distantly related species and exhibits the lowest similarity (96.2%) with Pedomicrobium americanum. Australian isolate Pedomicrobium sp. strain ACM 3067, P. americanum, and P. australicum are all very highly related, with similarities greater than 99%. Pedomicrobium sp. strain ACM 3067 is most closely related to P. australicum (level of similarity, 99.6%) and P. americanum (99.4%). These manganese-oxidizing species are more closely related to the iron-oxidizing species Pedomicrobium ferrugineum than to the other manganese-oxidizing species, P. manganicum. Taxonomic uncertainties resulting from the loss of the type culture of P. australicum are discussed.
BauidJ., TylerP. A.1971; Taxonomic implications of reproductive mechanisms of Hyphomicrobium-facies and Pedomicrobium-facies of a pleomorphic budding bacterium. Antonie Leeuwenhoek 37:417–424
BolietC., GevaudanM. J., de LamballerieX., ZandottiC., de MiccoP.1991; A simple method for the isolation of chromosomal DNA from Gram positive or acid-fast bacteria. Nucleic Acids Res 19:19–55
FoxG. E., WisotzkeyJ. D., JurtshukP.Jr.1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol 42:166–170
GebersR.1981; Enrichment, isolation, and emended description of Pedomicrobium ferrugineum Aristovskaya and Pedomicrobium manganicum Aristovskaya. Int. J. Syst. Bacteriol 31:302–316
GebersR., MandelM., HirschP.1981; Deoxyribonucleic acid base composition and nucleotide distribution of Pedomicrobium spp. Zentralbl. Bakteriol. Hyg. Abt. 1 Orig. G 2:332–338
GebersR., WehmeyerU., RoggentinT., SchlesnerH., Kolbel-BoelkeJ., HirschP.1985; Deoxyribonucleic acid base compositions and nucleotide distributions of 65 strains of budding bacteria. Int. J. Syst. Bacteriol 35:260–269
MurrayR. G. E., BrennerD. J., ColwellR. R., De VosP., GoodfellowM., GrimontP. A. D., PfennigN., StackebrandtE., ZavarzinG. A.1990; Report of the Ad Hoc Committee on Approaches to Taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol 40:213–215
RoggentinT., HirschP.1989; Ribosomal RNA cistron similarities among Hyphomicrobium species and several other hyphal, budding bacteria. Syst. Appl. Microbiol 11:140–147
RugerH. J., RichterG.1979; Bacillus psychrophilus Larkin and Stokes 1967, a later synonym of Bacillus globisporus Larkin and Stokes 1967. Int. J. Syst. Bacteriol 29:194–195
SlyL. L., ArunpairojanaV., HodgkinsonM. C.1988; Pedomicrobium manganicum from drinking-water distribution systems with manganese-related “dirty water” problems. Syst. Appl. Microbiol 11:75–84
StackebrandtE., FischerA., RoggentinT., WehmeyerU., BomarD., SmidaJ.1988; A phylogenetic survey of budding, and/or prosthecate, non-phototrophic eubacteria: membership of Hyphomicrobium, Hyphomonas, Pedomicrobium, Filomicrobium, Caulobacter and “Dichotomicrobium” to the alpha-subdivision of purple non-sulfur bacteria. Arch. Microbiol 149:547–556
StackebrandtE., GoebelB. M.1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol 44:846–849
WayneL. G., BrennerD. J., ColwellR. R., GrimontP. A. D., KandlerO., KrichevskyM. I., MooreL. H., MooreW. E. C., MurrayR. G. E., StackebrandtE., StarrM. P., TriiperH. G.1987; Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol 37:463–464