Advertisement

DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation

  • Ramon Rosselló-Mora

Abstract

DNA-DNA reassociation techniques are used for many purposes, but in the field of microbial systematics they are in most cases linked to the circumscription of prokaryotic species. Actually, as we will see, the use of whole genome hybridizations in the definition of prokaryotic species has had an enormous influence since the origin of the polythetic classification system (Rosselló-Mora and Kämpfer 2004). The importance of morphology in the middle of the eighteenth century was substituted for that of biochemical properties at the beginning of the nineteenth century; and subsequently the emerging “modern spectrum” techniques emphasized the importance of genetic measurements, such as DNA-DNA reassociation experiments. However, after almost 50 years of the application of these techniques to circumscribe species, there is increasing reluctance to use them because of the intrinsic pitfalls in the methods (e.g. Stackebrandt 2003; Stackebrandt et al. 2002). Consequently, the question that arises is: if DNA reassociation techniques are to be substituted, what will take their place? However, in my opinion, it is still too soon to substitute these techniques because of several reasons: (a) the use of such parameters in the definition of species has been of paramount influence and has actually determined the size and shape of what we call ‘species’, (b) there are almost 5,000 species described (Garrity et al. 2004), many of them based on reassociation experiments, and the legitimacy of new circumscription methods should be validated and (c) the alternatives proposed are not yet standardized and tested sufficiently enough to offer a reliable, pragmatic and easy to use circumscription tool.

Keywords

Species Concept Species Problem Prokaryotic Species Microbial Taxonomy Relative Binding Ratio 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adnan S, Li N, Miura H, Hashimoto Y, Yamamoto H, Ezaki T (1993) Covalently immobilized DNA plate for luminometric DNA-DNA hybridization to identify viridans streptococci in under 2 hours. FEMS Microbiol Lett 106:139–142CrossRefPubMedGoogle Scholar
  2. Amann RI, Lin C, Key R, Montgomery L, Stahl D (1992) Diversity among Fibrobacter isolates: Towards a phylogenetic classification. System Appl Microbiol 15:23–31Google Scholar
  3. Bolton ET, McCarthy BJ (1962) A general method for the isolation of RNA complementary to DNA. Proc Nat Acad Sci USA 48:1390–1397CrossRefPubMedGoogle Scholar
  4. Brenner DJ (1978) Characterization and clinical identification of Enterobacteriaceae by DNA hybridization. Prog Clin Pathol 7:71–17PubMedGoogle Scholar
  5. Brenner DJ, Cowie DB (1968) Thermal stability of Escherichia coli-Salmonella typhymurium deoxyribonucleic acid duplexes. J Bacteriol 95:2258–2262PubMedGoogle Scholar
  6. Brenner DJ, Fanning GR, Johnson KE, Citarella RV, Falkow S (1969a) Polynucleotide sequence relationships among members of Enterobacteriaceae. J Bacteriol 98:637–650PubMedGoogle Scholar
  7. Brenner DJ, Fanning GR, Rake AV, Johnson KE (1969b) Batch procedure for thermal elution of DNA from hydroxyapatite. Anal Biochem 28:447–459CrossRefPubMedGoogle Scholar
  8. Brigandt I (2002) Species pluralism does not imply species eliminativism. Phyl Sci 70:1305–1316CrossRefGoogle Scholar
  9. Cardinali G, Liti G, Martini A (2000) Non-radioactive dot-blot DNA reassociation for unequivocal yeast identification. Int J Syst Evol Microbiol 50:931–936PubMedGoogle Scholar
  10. Cho J-C, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67:3677–3682CrossRefPubMedGoogle Scholar
  11. Christensen H, Angen Ø, Mutters R, Olsen JE, Bisgaard M (2000) DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102PubMedGoogle Scholar
  12. Crosa JH, Brenner DJ, Falkow S (1973) Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo-and hetero-duplexes. J Bacteriol 115:904–911PubMedGoogle Scholar
  13. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefPubMedGoogle Scholar
  14. De Ley J, Tijtgat R (1970) Evaluation of membrane filter methods for DNA-DNA hybridization. Antonie Van Leeuwenhoek 36:461–474CrossRefPubMedGoogle Scholar
  15. Ereshefsky M (1994) Some problems with the Linnaean hierarchy. Phyl Sci 61:186–205CrossRefGoogle Scholar
  16. Ereshefsky M (1998) Species pluralism and anti-realism. Phyl Sci 65:103–120CrossRefGoogle Scholar
  17. Euzéby JP, Tindall BJ (2004) Valid publication of new names or new combinations: making use of the validation lists. ASM News 70:258–259Google Scholar
  18. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229CrossRefGoogle Scholar
  19. Fitch WM (2000) Homology: a personal view on some of the problems. Trends Genet 16:227–231CrossRefPubMedGoogle Scholar
  20. Fox GE, Wisotzkey JD, Jurtshuk P Jr (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170CrossRefPubMedGoogle Scholar
  21. Gade D, Schlesner H, Glöckner FO, Amann R, Pfeiffer S, Thomm M (2004) Identification of Planctomycetes with order-, genus-, and strain-specific 16S rRNA-targeted probes. Microbiol Ecol 47:243–251CrossRefGoogle Scholar
  22. Garrity GM, Bell JA, Lilburn TG (2004) Taxonomic outline of the Prokaryotes. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, rel 5.0. Springer, Berlin Heidelberg New York, DOI:10.1007/bergeysoutline200405Google Scholar
  23. Gillis M, Vandamme P, De Vos P, Swings J, Kersters K (2001) Polyphasic taxonomy. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, Berlin Heidelberg New York, pp 43–48Google Scholar
  24. González JM, Sáiz-Jiménez C (2004) A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 9:75–79CrossRefPubMedGoogle Scholar
  25. Goodfellow M, Manfio GP, Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman & Hall, London, pp 25–59Google Scholar
  26. Goris J, Suzuki K-I, De Vos P, Nakase T, Kersters K (1998) Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148–1153CrossRefGoogle Scholar
  27. Grimont PAD (1988) Use of DNA reassociation in bacterial classification. Can J Microbiol 34:541–546CrossRefPubMedGoogle Scholar
  28. Grimont PAD, Popoff MY, Grimont F. Coynault C, Lemelin M (1980) Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4:325–330CrossRefGoogle Scholar
  29. Hey J (2001) The mind of the species problem. Trends Ecol Evol 16:326–329CrossRefPubMedGoogle Scholar
  30. Hey J, Waples RS, Arnold ML, Butlin RK, Harrison RG (2003) Understanding and confronting species uncertainty in biology and conservation. Trends Ecol Evol 18:597–603CrossRefGoogle Scholar
  31. Hull DL (1997) The ideal species concept — and why we can’t get it. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman & Hall, London, pp 357–380Google Scholar
  32. Huß VAR, Festl H, Schleifer KH (1983) Studies on the spectrometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192Google Scholar
  33. Jahnke K-D (1994) A modified method of quantitative colorimetric DNA-DNA hybridization on membrane filters for bacterial identification. J Microbiol Methods 20:237–288CrossRefGoogle Scholar
  34. Johnson JL (1973) Use of nucleic acid homologies in the taxonomy of anaerobic bacteria. Int J Syst Bacteriol 23:308–315CrossRefGoogle Scholar
  35. Johnson JL (1981) Genetic characterization. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Philips GB (eds) Manual of methods for general microbiology. ASM, Washington, D.C., pp 450–472Google Scholar
  36. Johnson JL (1985) DNA reassociation and RNA hybridisation of bacterial nucleic acids. Methods Microbiol 18:33–74CrossRefGoogle Scholar
  37. Johnson JL (1989) Nucleic acids in bacterial classification. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams and Wilkins, Baltimore, pp 2306–2309Google Scholar
  38. Johnson JL (1991) DNA reassociation experiments. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, pp 21–44Google Scholar
  39. Jurado V, Láiz L, González JM, Hernández-Marine M, Valens M, Sáiz-Jimenez C (2005) Phyllobacterium catacumbae, sp. nov., a member of the Rhizobiales isolated from roman catacombs. Int J Syst Evol Microbiol (in press)Google Scholar
  40. Kaznowski A (1995) A method of colorimetric DNA-DNA hybridization in microplates with covalently immobilized DNA for identification of Aeromonas spp. Med Microbiol Lett 4:362–369Google Scholar
  41. Krieg N (1988) Bacterial classification: an overview. Can J Microbiol 34:536–540CrossRefPubMedGoogle Scholar
  42. Konstantinidis KT, Tiedje JM (2005) Genomic insights to advance the species definition for prokaryotic species. Proc Natl Acad Sci USA, DOI: 10.1073/pnas.0409727102Google Scholar
  43. Lind E, Ursing J (1986) Clinical strains of Enterobacter agglomerans (synonyms: Erwinia herbicola, Erwinia mellitiae) identified by DNA-DNA hybridization. Acta Pathol Microbiol Immunol Scand B 94:250–231Google Scholar
  44. Mallet J, Willmott K (2003) Taxonomy: renaissance of tower of Babel? Trends Ecol Evol 18:57–59CrossRefGoogle Scholar
  45. Martínez-Murcia AJ, Benlloch S, Collins MD (1992) Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16 s ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacteriol 42:412–421CrossRefPubMedGoogle Scholar
  46. Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge MF, Dawah HA, Wilson MR (eds.) Species: the units of biodiversity. Chapman & Hall, London, pp 381–421Google Scholar
  47. Mayr E (1942) Systematics and the origin of species from the view point of a zoologist. Columbia University, New YorkGoogle Scholar
  48. Mehlen A, Goeldner M, Ried S, Stindl S, Ludwig W, Schleifer K-H (2004) Development of a fast DNA-DNA hybridization method based on melting profiles in microplates. System Appl Microbiol 27:689–695CrossRefGoogle Scholar
  49. Mindell DP, Meyer A (2001) Homology evolving. Trends Ecol Evol 16:434–439CrossRefGoogle Scholar
  50. Mishler BD, Donoghue MJ (1982) Species concepts: a case for pluralism. Syst Zool 31:491–503CrossRefGoogle Scholar
  51. Owen RJ, Pitcher D (1985) Current methods for estimating DNA base composition and levels of DNA-DNA hybridization. In: Goodfellow M, Minikin E (eds) Chemical methods in bacterial systematics. Academic, London, pp 67–93Google Scholar
  52. Palleroni NJ (2003) Prokaryote taxonomy of the 20th century and the impact of studies on genus Pseudomonas: a personal view. Microbiology 149:1–7CrossRefPubMedGoogle Scholar
  53. Palys T, Nakamura LK, Cohan FM (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47:1145–1156CrossRefPubMedGoogle Scholar
  54. Popoff M, Coynault C (1980) Use of DEAE-cellulose filters in the S1 nuclease method for bacterial deoxyribonucleic acid hybridization. Ann Microbiol 131A:151–155Google Scholar
  55. Ramisse V, Balandreau J, Thibault F, Vidal D, Vergnaud G, Normand P (2003) DNA-DNA hybridization study of Burkholderia species using genomic DNA macro-array analysis coupled to reverse genome probing. Int J Syst Evol Microbiol 53:739–746CrossRefPubMedGoogle Scholar
  56. Ravin AW (1963) Experimental approaches to the study of bacterial phylogeny. Am Nat 97:307–318CrossRefGoogle Scholar
  57. Reydon TAC (2004) Why does the species problem still persist? Bioessays 26:300–305CrossRefPubMedGoogle Scholar
  58. Rosselló R, Garcia-Valdés E, Lalucat J, Ursing J (1991) Genotypic and phenotypic diversity of Pseudomonas stutzeri. System Appl Microbiol 14:150–157Google Scholar
  59. Rosselló-Mora R (2003) Opinion: the species problem, can we achieve a universal concept? System Appl Microbiol 26:323–326CrossRefGoogle Scholar
  60. Rosselló-Mora R, Amann, R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67CrossRefPubMedGoogle Scholar
  61. Rosselló-Mora R, Kämpfer P (2004) Defining microbial diversity — the species concept for prokaryotic and eukaryotic microorganisms. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM, Washington, D.C., pp 29–39Google Scholar
  62. Santos SR, Ochman H (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754–759CrossRefPubMedGoogle Scholar
  63. Schildkraut C, Lifson S (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3:195–208CrossRefPubMedGoogle Scholar
  64. Schildkraut CL, Marmur J, Doty P (1961) The formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol 3:595–617CrossRefPubMedGoogle Scholar
  65. Schleifer K-H, Stackebrandt E (1983) Molecular systematics of prokaryotes. Annu Rev Microbiol 37:143–187CrossRefPubMedGoogle Scholar
  66. Sneath PHA (1988) The phenetic and cladistic approaches. In: Hawksworth DL (ed) Prospects in systematics. Systematics Association/Clarendon, Oxford, pp 252–273Google Scholar
  67. Sneath PHA (1989) Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. System Appl Microbiol 12:15–31Google Scholar
  68. Sneath PHA (1992) International code of nomenclature of bacteria, 1990 revision. American Society for Microbiology, Washington, D.C.Google Scholar
  69. Stackebrandt E (2003) The richness of prokaryotic diversity: there must be a species some-where. Food Technol Biotechnol 41:17–22Google Scholar
  70. Stackebrandt E, Goebel BM (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 44:846–849CrossRefGoogle Scholar
  71. Stackebrandt E, Liesack W (1993) Nucleic acids and classification. In: Goodfellow M, O’Donnell AG (eds) Handbook of new bacterial systematics. Academic, London, pp 151–194Google Scholar
  72. Stackebrandt E, Frederiksen W, Garrity G, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047CrossRefPubMedGoogle Scholar
  73. Staley JT (2004) Speciation and bacterial phylospecies. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM, Washington, D.C., pp 40–48Google Scholar
  74. Tindall BJ (2002) Prokaryotic systematics: a theoretical overview. Encycl Life Sci 15:244–251Google Scholar
  75. Tjernberg I, Ursing J (1989) Clinical strains of Acinetobacter classified by DNA-DNA hybridization. APMIS 97:595–605CrossRefPubMedGoogle Scholar
  76. Tjernberg I, Lindth E, Ursing J (1989) A quantitative bacterial dot method for DNA-DNA hybridization and its correlation to the hydroxyapatite method. Curr Microbiol 18:77–81CrossRefGoogle Scholar
  77. Turner, DJ (1996) Thermodynamics of base pairing. Curr Opin Struct Biol 6:299–304CrossRefPubMedGoogle Scholar
  78. Ullman SJ, McCarthy BJ (1973) The relationship between mismatched base pairs and the thermal stability of DNA duplexes. Biochim Biophys Acta 294:416–424PubMedGoogle Scholar
  79. Ursing JB, Rosselló-Mora RA, Garcia-Valdes E, Lalucat J (1995) Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int J Syst Bacteriol 45:604CrossRefGoogle Scholar
  80. Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438PubMedGoogle Scholar
  81. Watanabe T, Murata Y, Oka S, Iwahashi H (2004) A new approach to species determination for yeast strains: DNA micro array-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes. Yeast 21:351–365CrossRefPubMedGoogle Scholar
  82. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  83. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583CrossRefPubMedGoogle Scholar
  84. Young JPW (1998) Bacterial evolution and the nature of species. In: Carvalho GR (ed) Advances in molecular ecology. IOS, Amsterdam, pp 119–131Google Scholar
  85. Young JM (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945–953PubMedGoogle Scholar
  86. Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900CrossRefPubMedGoogle Scholar
  87. Ziemke F, Höfle MG, Lalucat J, Rosselló-Mora R (1998) Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. Nov. Int J Syst Bacteriol 48:179–186CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Ramon Rosselló-Mora
    • 1
  1. 1.Grup d’Oceanografia InterdisciplinarInstitut Mediterrani d’Estudis Avançats (CSIC-UIB)Esporles, Illes BalearsSpain

Personalised recommendations