1887

Abstract

A phylogenetic analysis of -and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the (>14 % divergence) and (>16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that contained motifs atypical of the -, suggesting that it is ancestral to . While none of the strains were of marine origin, included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that be placed into a new genus, gen. nov., with A3.12 (=ATCC 15145=NCCB 72004) as its type strain. Also proposed is a redefinition of the and the lineages as two different families, i.e. ‘’ and a new family, . Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02978-0
2004-09-01
2019-12-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/5/ijs541439.html?itemId=/content/journal/ijsem/10.1099/ijs.0.02978-0&mimeType=html&fmt=ahah

References

  1. Baer, M. L., Ravel, J., Chun, J., Hill, R. T. & Williams, W. N. ( 2000; ). A proposal for the reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into a new genus, Bacteriovorax gen. nov., as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively. Int J Syst Evol Microbiol 50, 219–224.[CrossRef]
    [Google Scholar]
  2. Cannone, J. J., Subramanian, S., Schnare, M. N. & 11 other authors ( 2002; ). The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2.[CrossRef]
    [Google Scholar]
  3. Castro, H. F., Williams, N. H. & Ogram, A. ( 2000; ). Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31, 1–9.
    [Google Scholar]
  4. Cohan, F. M. ( 2002; ). What are bacterial species? Annu Rev Microbiol 56, 457–487.[CrossRef]
    [Google Scholar]
  5. Donze, D., Mayo, J. A. & Diedrich, D. L. ( 1991; ). Relationship among bdellovibrios revealed by partial sequences of 16S ribosomal RNA. Curr Microbiol 23, 115–119.[CrossRef]
    [Google Scholar]
  6. Felsenstein, J. ( 1992; ). Phylogenies from restriction sites – a maximum-likelihood approach. Evolution 46, 159–173.[CrossRef]
    [Google Scholar]
  7. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., 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.[CrossRef]
    [Google Scholar]
  8. Fuhrman, J. A. ( 1999; ). Marine viruses and their biogeochemical and ecological effects. Nature 399, 541–547.[CrossRef]
    [Google Scholar]
  9. Garrity, G. M., Johnson, K. L., Bell, J. A. & Searles, D. B. ( 2002; ). Taxonomic outline of the procaryotes. In Bergey's Manual of Systematic Bacteriology, 2nd edn. Release 3.0. New York: Springer.
  10. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. ( 1990; ). Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60–63.[CrossRef]
    [Google Scholar]
  11. Glöckner, F. O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A. & Amann, R. ( 2000; ). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66, 5053–5065.[CrossRef]
    [Google Scholar]
  12. Gutell, R. R., Lee, J. C. & Cannone, J. J. ( 2002; ). The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12, 301–310.[CrossRef]
    [Google Scholar]
  13. Heyndrickx, M., Vauterin, L., Vandamme, P., Kersters, K. & De Vos, P. ( 1996; ). Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods 26, 247–259.[CrossRef]
    [Google Scholar]
  14. Hoeniger, J. F., Ladwig, R. & Moor, H. ( 1972; ). The fine structure of “resting bodies” of Bdellovibrio sp. strain W developed in Rhodospirillum rubrum. Can J Microbiol 18, 87–92.[CrossRef]
    [Google Scholar]
  15. Jürgens, K., Pernthaler, J., Schalla, S. & Amann, R. ( 1999; ). Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl Environ Microbiol 65, 1241–1250.
    [Google Scholar]
  16. Jurkevitch, E. ( 2000; ). The genus Bdellovibrio. In The Prokaryotes. Edited by M. Dworkin, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer (http://141.150.157.117:8080/prokPUB/index.htm).
  17. Jurkevitch, E. & Ramati, B. ( 2000; ). Design and uses of a Bdellovibrio 16S rRNA-targeted oligonucleotide. FEMS Microbiol Lett 184, 265–271.[CrossRef]
    [Google Scholar]
  18. Jurkevitch, E., Minz, D., Ramati, B. & Barel, G. ( 2000; ). Prey range characterization, ribotyping, and diversity of soil and rhizosphere Bdellovibrio spp. isolated on phytopathogenic bacteria. Appl Environ Microbiol 66, 2365–2371.[CrossRef]
    [Google Scholar]
  19. Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M. & Schleifer, K. H. ( 1998; ). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19, 554–568.[CrossRef]
    [Google Scholar]
  20. Marchesi, J. R., Sato, T., Weightman, A. J., Martin, T. A., Fry, J. C., Hiom, S. J., Dymock, D. & Wade, W. G. ( 1998; ). Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64, 795–799.
    [Google Scholar]
  21. Martin, M. O. ( 2002; ). Predatory prokaryotes: an emerging research opportunity. J Mol Microbiol Biotechnol 4, 467–477.
    [Google Scholar]
  22. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. ( 1999; ). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911–940.[CrossRef]
    [Google Scholar]
  23. Moulder, J. W. ( 1985; ). Comparative biology of intracellular parasitism. Microbiol Rev 49, 298–337.
    [Google Scholar]
  24. Philippe, H. & Laurent, J. ( 1998; ). How good are deep phylogenetic trees? Curr Opin Genet Dev 8, 616–623.[CrossRef]
    [Google Scholar]
  25. Ronn, R., McCaig, A. E., Griffiths, B. S. & Prosser, J. I. ( 2002; ). Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68, 6094–6105.[CrossRef]
    [Google Scholar]
  26. Rossello-Mora, R. & Amann, R. ( 2001; ). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39–67.[CrossRef]
    [Google Scholar]
  27. Sanchez-Amat, A. & Torrella, F. ( 1990; ). Formation of stable bdelloplasts as a starvation survival strategy of marine bdellovibrios. Appl Environ Microbiol 56, 2717–2725.
    [Google Scholar]
  28. Schwudke, D., Strauch, E., Krueger, M. & Appel, B. ( 2001; ). Taxonomic studies of predatory bdellovibrios based on 16S rRNA analysis, ribotyping and the hit locus and characterization of isolates from the gut of animals. Syst Appl Microbiol 24, 385–394.[CrossRef]
    [Google Scholar]
  29. Seidler, R. J., Mandel, M. & Baptist, J. N. ( 1972; ). Molecular heterogeneity of the bdellovibrios: evidence of two new species. J Bacteriol 109, 209–217.
    [Google Scholar]
  30. Snyder, A. R., Williams, H. N., Baer, M. L., Walker, K. E. & Stine, O. C. ( 2002; ). 16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity. Int J Syst Evol Microbiol 52, 2089–2094.[CrossRef]
    [Google Scholar]
  31. Stackebrandt, E. & Goebel, B. 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.[CrossRef]
    [Google Scholar]
  32. Stolp, H. & Starr, M. P. ( 1963; ). Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie Van Leeuwenhoek 29, 217–248.[CrossRef]
    [Google Scholar]
  33. Strunk, O., Gross, O., Reichel, B. & 11 other authors ( 1999; ). arb: a software environment for sequence data (http://www.mikro.biologie.tu-muenchen.de). Munich: Department of Microbiology, Technische Universität München.
  34. Teske, A., Wawer, C., Muyzer, G. & Ramsing, N. B. ( 1996; ). Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol 62, 1405–1415.
    [Google Scholar]
  35. Torsvik, V., Ovreas, L. & Thingstad, T. F. ( 2002; ). Prokaryotic diversity – magnitude, dynamics, and controlling factors. Science 296, 1064–1066.[CrossRef]
    [Google Scholar]
  36. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. ( 1996; ). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438.
    [Google Scholar]
  37. Varon, M. & Shilo, M. ( 1980; ). Ecology of aquatic bdellovibrios, pp. 1–48. In Advances in Aquatic Microbiology, vol. 2. Edited by M. R. Droop & H. W. Jannasch. New York: Academic Press.
  38. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
  39. Williams, H. N., Scheoffield, A. J., Guether, D., Kelley, J., Shah, D. & Falker, W. A. ( 1995; ). Recovery of bdellovibrios from submerged surfaces and other aquatic habitats. Microb Ecol 29, 39–48.
    [Google Scholar]
  40. Woese, C. R. ( 1987; ). Bacterial evolution. Microbiol Rev 51, 221–271.
    [Google Scholar]
  41. Wright, T. D., Vergin, K. L., Boyd, P. W. & Giovannoni, S. J. ( 1997; ). A novel δ-subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microbiol 63, 1441–1448.
    [Google Scholar]
  42. Wuyts, J., Van de Peer, Y., Winkelmans, T. & De Wachter, R. ( 2002; ). The European database on small subunit ribosomal RNA. Nucleic Acids Res 30, 183–185.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.02978-0
Loading
/content/journal/ijsem/10.1099/ijs.0.02978-0
Loading

Data & Media loading...

Supplements

vol. , part 5, pp. 1439–1452

Details of sequences of environmental clones exhibiting homology to BALOs, and 16S rRNA secondary-structure models, are available to download. [PDF](255 KB)



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error