Phylogenetic differentiation of two closely related Nitrosomonas spp. that inhabit different sediment environments in an oligotrophic freshwater lake

Applied and Environmental Microbiology

Volumn 65, Issue 11, 1999, Pages 4855-4862

  Whitby, Corinne B ^a   Saunders, Jon R ^a   Rodriguez, Juana ^a   Pickup, Roger W ^b   McCarthy, Alan ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; BACTERIAL DNA; BACTERIAL RNA; FRESH WATER; LAKE WATER; RIBOSOME DNA; RIBOSOME RNA;

BACTERIUM; LACUSTRINE DEPOSIT; PHYLOGENETICS;

ARTICLE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; GENOTYPE; NITROSOMONAS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEASONAL VARIATION;

NITROSOMONAS; NITROSOMONAS EUROPAEA; NITROSOMONAS EUTROPHA; NITROSOSPIRA;

EID: 0032705903     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.11.4855-4862.1999     Document Type: Article

References (47)

1. Aakra, A., J. B. Utåker, and I. F. Nes. 1999. Restriction fragment length polymorphism of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidising bacteria: a phylogenetic approach. Int. J. Syst. Bacteriol. 49:123-130.
2. Bruce, K. D., W. D. Hiorns, J. L. Hobman, A. M. Osborn, P. Strike, and D. A. Ritchie. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl. Environ. Microbiol. 58:3413-3416.
3. Bruce, K. D. 1997. Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 63:4914-4919.
4. Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence-analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
5. Edwards, U., T. Rogall, H. Blöcker, M. Emde, and E. C. Böttger. 1989. Isolation and direct complete nucleotide determination of entire genes. Characterisation of a gene encoding 16S ribosomal RNA. Nucleic Acids Res. 17:7843-7853.
6. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle.
7. Freshwater Biological Association. 1998. Annual reports 1938-1998. Freshwater Biological Association, Ambleside, United Kingdom.
8. Hall, G. H. 1986. Nitrification in lakes, p. 127-156. In J. I. Prosser (ed.), Nitrification. IRL Press, Oxford, United Kingdom.
9. Hastings, R. C., M. T. Ceccherini, N. Miclaus, J. R. Saunders, M. Bazzicalupo, and A. J. McCarthy. 1997. Direct molecular biological analysis of ammonia-oxidising bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23:45-54.
10. Hastings, R. C., J. R. Saunders, G. H. Hall, R. W. Pickup, and A. J. Mc-Carthy. 1998. Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl. Environ. Microbiol. 64:3674-3682.
11. Head, I. M., W. D. Hiorns, T. M. Embley, A. J. McCarthy, and J. R. Saunders. 1993. The phylogeny of autotrophic ammonia-oxidising bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J. Gen. Microbiol. 139:1147-1153.
12. Hiorns, W. D., R. C. Hastings, I. M. Head, A. J. McCarthy, J. R. Saunders, R. W. Pickup, and G. H. Hall. 1995. Amplification of 16S ribosomal RNA genes of the autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of Nitrosospiras in the environment. Microbiology 141:2793-2800.
13. Hovanec, T. A., and E. F. DeLong. 1996. Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl. Environ. Microbiol. 62:2888-2896.
14. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
15. Kowalchuk, G. A., J. R. Stephen, W. De Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1489-1497.
16. Kowalchuk, G. A., Z. S. Naoumenko, P. Derikx, A. Felske, J. R. Stephen, and I. A. Arkhipchenko. 1999. Molecular analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in compost and composted materials. Appl. Environ. Microbiol. 65:396-403.
17. McCaig, A. E., T. M. Embley, and J. I. Prosser. 1994. Molecular analysis of enrichment cultures of marine ammonia-oxidisers. FEMS Microbiol. Lett. 120:363-368.
18. McCaig, A. E., C. J. Phillips, J. R. Stephen, G. A. Kowalchuk, S. M. Harvey, R. A. Herbert, T. M. Embley, and J. I. Prosser. 1999. Nitrogen cycling and community structure of proteobacterial β-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl. Environ. Microbiol. 65:213-220.
19. McTavish, H., J. A. Fuchs, and A. B. Hooper. 1993. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 175:2436-2444.
20. Mobarry, B. K., M. Wagner, V. Urbain, B. E. Rittmann, and D. A. Stahl. 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62:2156-2162.
21. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
22. Navarro, E., P. Simonet, P. Norman, and R. Bardin. 1992. Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch. Microbiol. 157:107-115.
23. Norton, J. M., J. M. Low, and M. G. Klotz. 1996. The gene encoding ammonia-monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 139:181-188.
24. Ohnstad, F. R., and J. G. Jones. 1982. The Jenkin surface mud sampler. User manual. Freshwater Biological Association annual report no. 15. Freshwater Biological Association, Ambleside, United Kingdom. (Occasional publication.)
25. Olsen, G. J., N. Larsen, and C. R. Woese. 1991. The ribosomal RNA database project (RDP). Nucleic Acids Res. 19(Suppl.):2017-2021.
26. Osborn, A. M., K. D. Bruce, P. Strike, and D. A. Ritchie. 1993. Polymerase chain reaction-restriction length polymorphism analysis shows divergence among mer determinants from gram-negative soil bacteria indistinguishable by DNA-DNA hybridization. Appl. Environ. Microbiol. 59:4024-4030.
27. Phillips, C. J., Z. Smith, T. M. Embley, and J. I. Prosser. 1999. Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in the northwestern Mediterranean Sea. Appl. Environ. Microbiol. 65:779-786.
28. Pommerening-Röser, A., G. Rath, and H.-P. Koops. 1996. Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19:344-351.
29. Prosser, J. I. 1989. Autotrophic nitrification in bacteria. Adv. Microb. Physiol. 30:125-181.
30. Rotthauwe, J.-H., K.-P. Witzel, and W. Liesack. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of the natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-4712.
31. Saitou, N., and M. Nei. 1987. The neighbour joining method; a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
32. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
33. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:437-4378.
34. Sinigalliano, C. D., D. N. Kuhn, and R. D. Jones. 1995. Amplification of the amoA gene from diverse species of ammonia-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl. Environ. Microbiol. 61:2702-2706.
35. Speksnijder, A., G. A. Kowalchuk, K. Roest, and H. Laanbroek. 1998. Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Syst. Appl. Microbiol. 21:321-330.
36. Stehr, G., B. Bottcher, P. Dittberner, G. Rath, and H.-P. Koops. 1995. The ammonia-oxidizing nitrifying populations of the River Elbe estuary. FEMS Microbiol. Ecol. 17:177-186.
37. Stephen, J. R., A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley. 1996. Molecular diversity of soil and marine 16S rRNA gene sequences related to β-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62:4147-4154.
38. Stephen, J. R., G. A. Kowalchuk, M.-A. V. Bruns, A. E. McCaig, C. J. Phillips, T. M. Embley, and J. I. Prosser. 1998. Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:2958-2965.
39. Stephen, J. R., Y.-J. Chang, S. J. Macnaughton, G. A. Kowalchuk, K. T. Leung, C. A. Flemming, and D. C. White. 1999. Effect of toxic metals on indigenous soil β-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl. Environ. Microbiol. 65:95-101.
40. Suwa, Y., T. Sumino, and K. Noto. 1997. Phylogenetic relationships of activated sludge isolates of ammonia-oxidisers with different sensitivities to ammonium sulphate. J. Gen. Appl. Microbiol. 43:373-379.
41. Teske, A., E. Alm, J. M. Regan, S. Toze, B. E. Rittmann, and D. A. Stahl. 1994. Evolutionary relationships among ammonia-and nitrite-oxidizing bacteria. J. Bacteriol. 176:6623-6630.
42. Atåker, J. B., L. R. Bakken, Q. Q. Jiang, and I. F. Nes. 1995. Phylogenetic analysis of seven new isolates of the highly related ammonia-oxidising bacteria based on 16S rRNA gene sequences. Syst. Appl. Microbiol. 18:549-559.
43. Utåker, J. B., and L. F. Nes. 1998. A qualitative evaluation of the published oligonucleotide specific for the 16S rRNA gene sequences of the ammonia-oxidising bacteria. Syst. Appl. Microbiol. 21:1-17.
44. Wagner, M., G. Rath, R. Amann, H.-P. Koops, and K.-H. Schleifer. 1995. In situ identification of ammonia-oxidising bacteria. Syst. Appl. Microbiol. 18: 251-264.
45. Ward, B. B. 1995. Diversity of culturable denitrifying bacteria-limits of rDNA RFLP analysis and probes for the functional gene, nitrite reductase. Arch. Microbiol. 163:167-175.
46. Ward, B. B., M. A. Voytek, and K.-P. Witzel. 1997. Phylogenetic diversity of natural populations of ammonia-oxidisers investigated by specific PCR amplification. Microb. Ecol. 33:87-96.
47. Watson, S. W., and M. Mandel. 1971. Comparisons of the morphology and deoxyribonucleic acid components of 27 strains of nitrifying bacteria. J. Bacteriol. 107:563-569.