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. 1996 Nov;62(11):4147–4154. doi: 10.1128/aem.62.11.4147-4154.1996

Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria.

J R Stephen 1, A E McCaig 1, Z Smith 1, J I Prosser 1, T M Embley 1
PMCID: PMC168236  PMID: 8900005

Abstract

We have conducted a preliminary phylogenetic survey of ammonia-oxidizing beta-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing beta-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonas-like sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types.

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Selected References

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  1. Belser L. W. Population ecology of nitrifying bacteria. Annu Rev Microbiol. 1979;33:309–333. doi: 10.1146/annurev.mi.33.100179.001521. [DOI] [PubMed] [Google Scholar]
  2. Belser L. W., Schmidt E. L. Diversity in the ammonia-oxidizing nitrifier population of a soil. Appl Environ Microbiol. 1978 Oct;36(4):584–588. doi: 10.1128/aem.36.4.584-588.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cilia V., Lafay B., Christen R. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol. 1996 Mar;13(3):451–461. doi: 10.1093/oxfordjournals.molbev.a025606. [DOI] [PubMed] [Google Scholar]
  4. Embley T. M. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol. 1991 Sep;13(3):171–174. doi: 10.1111/j.1472-765x.1991.tb00600.x. [DOI] [PubMed] [Google Scholar]
  5. Farrelly V., Rainey F. A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol. 1995 Jul;61(7):2798–2801. doi: 10.1128/aem.61.7.2798-2801.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. doi: 10.1038/345060a0. [DOI] [PubMed] [Google Scholar]
  7. Head I. M., Hiorns W. D., Embley T. M., McCarthy A. J., Saunders J. R. The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J Gen Microbiol. 1993 Jun;139(Pt 6):1147–1153. doi: 10.1099/00221287-139-6-1147. [DOI] [PubMed] [Google Scholar]
  8. Hiorns W. D., Hastings R. C., Head I. M., McCarthy A. J., Saunders J. R., Pickup R. W., Hall G. H. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment. Microbiology. 1995 Nov;141(Pt 11):2793–2800. doi: 10.1099/13500872-141-11-2793. [DOI] [PubMed] [Google Scholar]
  9. Koops H. P., Harms H. Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria. Arch Microbiol. 1985 Apr;141(3):214–218. doi: 10.1007/BF00408061. [DOI] [PubMed] [Google Scholar]
  10. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. McCaig A. E., Embley T. M., Prosser J. I. Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett. 1994 Jul 15;120(3):363–367. doi: 10.1111/j.1574-6968.1994.tb07059.x. [DOI] [PubMed] [Google Scholar]
  12. Murray R. G., Stackebrandt E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol. 1995 Jan;45(1):186–187. doi: 10.1099/00207713-45-1-186. [DOI] [PubMed] [Google Scholar]
  13. Neefs J. M., Van de Peer Y., De Rijk P., Chapelle S., De Wachter R. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 1993 Jul 1;21(13):3025–3049. doi: 10.1093/nar/21.13.3025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Prosser J. I. Autotrophic nitrification in bacteria. Adv Microb Physiol. 1989;30:125–181. doi: 10.1016/s0065-2911(08)60112-5. [DOI] [PubMed] [Google Scholar]
  15. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  16. Schmidt T. M., DeLong E. F., Pace N. R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991 Jul;173(14):4371–4378. doi: 10.1128/jb.173.14.4371-4378.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Stahl D. A., Flesher B., Mansfield H. R., Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol. 1988 May;54(5):1079–1084. doi: 10.1128/aem.54.5.1079-1084.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Suzuki M. T., Giovannoni S. J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol. 1996 Feb;62(2):625–630. doi: 10.1128/aem.62.2.625-630.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Teske A., Alm E., Regan J. M., Toze S., Rittmann B. E., Stahl D. A. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J Bacteriol. 1994 Nov;176(21):6623–6630. doi: 10.1128/jb.176.21.6623-6630.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Tsai Y. L., Olson B. H. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol. 1992 Jul;58(7):2292–2295. doi: 10.1128/aem.58.7.2292-2295.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Voytek M. A., Ward B. B. Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl Environ Microbiol. 1995 Apr;61(4):1444–1450. doi: 10.1128/aem.61.4.1444-1450.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Walsh P. S., Metzger D. A., Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991 Apr;10(4):506–513. [PubMed] [Google Scholar]

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