Skip to main content
SpringerLink
Log in

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

  • Original Papers
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

The phylogenetic position of various budding and/or prosthecate Gram-negative eubacteria was determined by different methods. Members of the genera Hyphomicrobium, Filomicrobium, Pedomicrobium were investigated by 16S rRNA cataloguing, a 1373 nucleotide long portion of the 16S rRNA was sequenced from Hyphomicrobium vulgare and the 5S rRNAs were analyzed from two Hyphomicrobium strains, Hyphomonas polymorpha and Caulobacter crescentus. Comparison with published sequences indicated a membership of all of these organisms to the alpha subdivision of purple bacteria. While C. crescentus and Hyphomonas polymorpha constitute separate individual lines of descent, the position of a coherent cluster embracing Hyphomicrobium, Pedomicrobium and Filomicrobium is not yet settled. 16S rRNA cataloguing indicate the presence of a distinct line equivalent to other subgroups in its phylogenetic depth. 5S rRNA analysis, on the other hand, groups Hyphomicrobium vulgare and strain IFAM 1761 with members of subgroup alpha-2 (Rhodopseudomonas palustris, Nitrobacter winogradskyi and relatives). In contrast to the present classification, Pedomicrobium ferrugineum and Filimicrobium fusiforme are more closely related to certain Hyphomicrobium strains than these are related among each other. Budding mode of reproduction and prosthecate morphology are dominating morphological features of members of the alpha subdivision. These characteristics may gain diagnostic significance in a future formal description of this subdivision and its subgroups as a higher rank.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Albrecht W, Fischer A, Smida J, Stackebrandt E (1987) Verrucomicrobium spinosum, a eubacterium representing an ancient line of descent. System Appl Microbiol 10:57–62

    Google Scholar 

  • Bomar D, Stackebrandt E (1987) 5S rRNA sequences from Nitrobacter winogradskyi, Caulobacter crescentus, Stella humosa and Verrucomicrobium spinosum. Nucl Acids Res 15:9597

    Google Scholar 

  • Bomar D, Giovannoni S, Stackebrandt E (1987) A new type of eubacterial 5S rRNA in members of the order Planctomycetales. J Mol Evol (in press)

  • Brosius J, Palmer JL, Kennedy JP, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Nat Acad Sci (USA) 75:4801–4805

    Google Scholar 

  • Buchanan RE, Gibbons NE (1974) Budding and/or appendaged bacteria. In: Buchanan RE, Gibbons NE (eds) Bergey's manual of determinative bacteriology, 8th edn. Williams and Wilkins, Baltimore, p 148

    Google Scholar 

  • Chen EG, Seeburg PH (1985) Supercoil sequencing: a fast and simple method for sequencing plasmid DNA DNA 4:165–170

    Google Scholar 

  • Corder RE, Magruder GC, Clausen EC, Gaddy JL (1987) Isolation and characterization of a prosthecate methylotroph. Abstract I-138 of the 87th ASM Meeting, 1–6 March, Atlanta, USA

  • De Wachter R, Huysmans E, Vandenberghe A (1985) 5S ribosomal RNA as a tool for studying evolution. In: Schleifer KH, Stackebrandt E (eds) Evolution of prokaryotes. Academic Press. London, pp 115–141

    Google Scholar 

  • Donis-Keller H, Maxam AM, Gilbert W (1977) Mapping adenines, guanines and pyrimidines in RNA. Nucl Acids Res 4:2527–2538

    Google Scholar 

  • Eckhardt FEW, Roggentin P, Hirsch P (1979) Fatty acid composition of various hyphal budding bacteria. Arch Microbiol 120:81–85

    Google Scholar 

  • Embley M, Smida J, Stackebrandt E (1988) Reverse transcriptase sequencing of 16S rRNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta. J Gen Microbiol (in press)

  • Erdmann VA, Wolters J (1986) Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences. Nucl Acids Res 14:1–59 Suppl

    Google Scholar 

  • Fischer A, Roggentin T, Schlesner H, Stackebrandt E (1985) 16S ribosomal RNA oligonucleotide cataloguing and the phylogenetic position of Stella humosa. System Appl Microbiol 6:43–47

    Google Scholar 

  • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome C sequences is of general applicability. Science 155:279–284

    Google Scholar 

  • Fowler VJ, Pfennig N, Schubert W, Stackebrandt E (1984) Towards a phylogeny of phototrophic purple sulfur bacteria-16S rRNA oligonucleotide cataloguing of 11 species of Chromatiaceae. Arch Microbiol 139:382–387

    Google Scholar 

  • Fox GE, Stackebrandt E (1987) The application of 16S rRNA cataloguing and 5S rRNA sequencing in bacterial systematics. In: Colwell R, Grigorova R (eds) Methods in microbiology, vol 19. Academic Press, Orlando, pp 405–458

    Google Scholar 

  • Fox GE, Pechman KJ, Woese CR (1977) Comparative cataloging of 16S ribosomal ribonucleic acid: a molecular approach to prokaryotic systematics. Int J System Bacteriol 27:44–57

    Google Scholar 

  • Gebers R (1981) Enrichment, isolation, and emended description of Pedomicrobium ferrungineum Aristovskaya and Pedomicrobium manganicum Aristovskaya. Int J System Bacteriol 31:302–316

    Google Scholar 

  • Gebers R, Wehmeyer U, Roggentin T, Schlesner H, Kölbel-Boelke J, Hirsch P (1985) Deoxyribonucleic acid base compositions and nucleotide distribution of 65 strains of budding bacteria. Int J Syst Bacteriol 35:260–269

    Google Scholar 

  • Gebers R, Martens B, Wehmeyer U, Hirsch P (1986) Deoxyribonucleic acid homologies of Hyphomicrobium spp., Hyphomonas ssp., and other hyphal, budding bacteria. Int J Syst Bacteriol 36:241–245

    Google Scholar 

  • Gibbons NE, Murray RGE (1978) Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 28:1–6

    Google Scholar 

  • Gibson J, Stackebrandt E, Zablen LB, Gupta C, Woese CR (1979) A phylogenetic analyses of the purple photosynthetic bacteria. Curr Microbiol 3:59–64

    Google Scholar 

  • Giovannoni SJ, Schabtach E, Castenholz RW (1987) Isophaera pallida, gen, and comb. nov., a gliding, budding eubacterium from hot springs. Arch Microbiol 147:276–284

    Google Scholar 

  • Hennecke H, Kaluza K, Thony B, Fuhrmann N, Ludwig W, Stackebrandt E (1985) Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen fixing bacteria. Arch Microbiol 142:342–348

    Google Scholar 

  • Henrici AT, Johnson DE (1935) Studies of freshwater bacteria. II. Stalked bacteria, a new order of Schizomyces. J Bacteriol 30:61–93

    Google Scholar 

  • Hirsch P (1974) Budding bacteria. Ann Rev Microbiol 28:391–444

    Google Scholar 

  • Hirsch P (1980) Distribution and pure culture studies of morphologically distinct solar lake microorganisms. In: Nissenbaum A (ed) Hypersaline brines and evaporitic environments. Elsevier/ North-Holland Sci Publ Co, Amsterdam, pp 41–60

    Google Scholar 

  • Hirsch P, Conti SF (1964) Biology of budding bacteria II. Growth and nutrition of Hyphomicrobium spp. Arch Mikrobiol 48:358–367

    Google Scholar 

  • Hirsch P, Müller M, Schlesner H (1977) New aquatic budding and prosthecate bacteria and their taxonomic position. Soc Appl Bacteriol Symp 6:107–133

    Google Scholar 

  • Hori H (1975) Evolution of 5S RNA. J Mol Evol 7:75–88

    Google Scholar 

  • Hori H, Osawa S (1986) Evolution change in 5S rRNA secondary structure and a phylogenetic tree of 352 5S rRNA species. Bio Systems 19:163–172

    Google Scholar 

  • Johnson JL (1981) Genetic characterization. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Briggs Phillips G (eds) Manual of methods for general bacteriology, Americ Soc Microbiol Washington, pp 450–475

    Google Scholar 

  • Kirby KS (1968) Isolation of nucleic acids with phenolic solvents. In: Grossmann L, Moldave K (eds) Methods in enzymology, vol XIIB. Academic Press. New York London, pp 87–99

    Google Scholar 

  • Krupp G, Gross HJ (1983) Sequence analysis of in vitro 32P-labeled RNA. In: Agris PF, Kopper RA (eds) The modified nucleotides of transfer RNA, II. Liss, New York, pp 11–58

    Google Scholar 

  • Lane O, Pace B, Olsen G, Stahl O, Sogin M, Pace N (1985a) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Nat Acad Sci 82:6955–6959

    Google Scholar 

  • Lane DJ, Stahl DA, Olsen GJ, Heller DJ, Pace NR (1985b) Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences. J Bacteriol 163:75–81

    Google Scholar 

  • Matzen N, Hirsch P (1982) Improved growth conditions for Hyphomicrobium sp B-522 and two additional strains. Arch Microbiol 131:32–35

    Google Scholar 

  • Moore RL (1977) Ribosomal ribonucleic acid cistron homologies among Hyphomicrobium and various other bacteria. Can J Microbiol 23:478–481

    Google Scholar 

  • Oyaizu H, Woese CR (1985) Phylogenetic relationships among the sulfate respiring bacteria, myxobacteria and purple bacteria. System Appl Microbiol 6:257–263

    Google Scholar 

  • Pfennig N, Trüper HG (1974) The phototrophic bacteria. In: Buchanan RE, Gibbons NE (eds) Bergey's manual of determinative bacteriology. Williams & Wilkins, Baltimore, pp 24–75

    Google Scholar 

  • Qu LH, Michot B, Bachellerie GP (1983) Improved methods for structure probing in large RNAs: a rapid heterologous sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5′ terminal domain of eukaryotic 28s rRNA. Nucl Acids Res 11:5903–5920

    Google Scholar 

  • Queen C, Korn LJ (1984) A comprehensive sequence analysis program for the IBM personal computer. Nucl Acids Res 12:581–599

    Google Scholar 

  • Rothe B, Fischer A, Hirsch P, Sitting M, Stackebrandt E (1987) The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen. nov. sp. nov. Arch Mikrobiol 147:92–99

    Google Scholar 

  • Schlesner H (1987) Filomicrobium fusiforme gen. nov., sp. nov., a slender budding, hyphal bacterium from brackish water. System Appl Microbiol 9:(in press)

  • Schmidt JM, Starr MP (1981) The Blastocaulis-Planctomyces group of budding and appendaged bacteria. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes, vol I. Springer, Berlin Heidelberg New York, pp 498–504

    Google Scholar 

  • Seewaldt E, Schleifer KH, Bock E, Stackebrandt E (1982) The close phylogenetic relationship of Nitrobacter and Rhodopseudomonas palustris. Arch Mikrobiol 131:287–290

    Google Scholar 

  • Stackebrandt E, Kroppenstedt R (1987) Union of the genera Actinoplanes Couch, Ampullariella Couch, and Amorphosporangium Couch in a redefined genus Actinoplanes. System Appl Microbiol 9:110–114

    Google Scholar 

  • Stackebrandt E, Woese CR (1984) The phylogeny of prokaryotes. Microbiol Sci 1:117–122

    Google Scholar 

  • Stackebrandt E, Ludwig W, Schleifer KH, Gros HJ (1981) Rapid cataloguing of ribonuclease T1 resistant oligonucleotides from ribosomal RNAs for phylogenetic studies. J Mol Evol 17:227–236

    Google Scholar 

  • Stackebrandt E, Ludwig W, Fox GE (1985) 16S ribosomal RNA oligonucleotide cataloguing. In: Gottschalk G (ed) Methods in microbiology, vol 18. Academic Press, London New York, pp 75–107

    Google Scholar 

  • Stackebrandt E, Fischer A, Hirsch P, Roggentin T, Schlesner H (1986) The phylogeny of an ancient group of budding peptidoglycan-less eubacteria: the genera Planctomyces and Pirella. Endocyt C Res 3:29–40

    Google Scholar 

  • Stackebrandt E, Ludwig W, Weizenegger M, Dorn S, McGill TJ, Fox GE, Woese CR, Schubert W, Schleifer KH (1987) Comparative 16S rRNA oligonucleotide analyses and murein types of round-spore-forming bacilli and non-spore-forming relatives. J Gen Microbiol 133:2523–2529

    Google Scholar 

  • Staley JT, Hirsch P, Schmidt JM (1981) Introduction to the budding and/or appendaged bacteria. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes, vol I. Springer, Berlin Heidelberg New York, pp 448–455

    Google Scholar 

  • Weisburg WG, Woese CR, Dobson ME, Weiss E (1985) A common origin of rickettsiae and certain plant pathogens. Sci 230:556–558

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    Google Scholar 

  • Woese CR, Stackebrandt E, Weisburg WG, Paster BJ, Madigan MT, Fowler VJ, Hahn CM, Blanz P, Gupta R, Nealson KH, Fox GE (1984) The phylogeny of purple bacteria: the alpha subdivision. System Appl Microbiol 5:315–326

    Google Scholar 

  • Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR (1985) Mitochondrial origins. Proc Natl Acad Sci (USA) 82:4443–4447

    Google Scholar 

  • Zavarzin GA (1961) Budding bacteria. Microbiology USSR 30:952–975

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut für Allgemeine Mikrobiologie, Christian Albrecht Universität, Olshausenstrasse 40, D-2300, Kiel, Germany

    Erko Stackebrandt, Angelika Fischer, Telse Roggentin, Uta Wehmeyer, Daniel Bomar & Jan Smida

Authors
  1. Erko Stackebrandt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Angelika Fischer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Telse Roggentin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Uta Wehmeyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Daniel Bomar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jan Smida
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Dedicated to Prof. Dr. P. Hirsch on the occasion of his 60th birthday

Rights and permissions

Reprints and permissions

About this article

Cite this article

Stackebrandt, E., Fischer, A., Roggentin, T. et al. 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 (1988). https://doi.org/10.1007/BF00446759

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00446759

Key words

Search

Navigation