Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands)

FEMS Microbiology Ecology

Volumn 31, Issue 3, 2000, Pages 207-215

  Kowalchuk, George A ^a   Stienstra, Atie W ^a   Heilig, G Hans J ^a   Stephen, John R ^b   Woldendorp, Jan W ^a  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Subgroup Proteobacteria; DGGE; Most probable number (MPN); Nitrification; Nitrosomonas; Nitrosospira; Oligonucleotide hybridisation; Soil pH

Indexed keywords

AMMONIA; RIBOSOME DNA;

BACTERIUM; COMMUNITY STRUCTURE; GRASSLAND SOIL;

ARTICLE; BACTERIUM IDENTIFICATION; DNA SEQUENCE; GEL ELECTROPHORESIS; MOLECULAR CLONING; MOLECULAR HYBRIDIZATION; NITRIFICATION; NITROSOMONAS; NITROSOSPIRA; NONHUMAN; PH; PHYLOGENY; PRIORITY JOURNAL; SOIL;

NETHERLANDS;

NITROSOMONAS; NITROSOSPIRA;

EID: 0034009793     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(99)00099-9     Document Type: Article

References (37)

1. Stienstra A.W., Klein-Gunnewiek P., Laanbroek H.J. Repression of nitrification in soils under a climax grassland vegetation. FEMS Microbiol. Ecol. 14:1994;45-52.
2. Felske A., Wolterink A., van Lis R., Akkermans A.D.L. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64:1998;871-879.
3. Belser L.W. Population ecology of nitrifying bacteria. Annu. Rev. Microbiol. 33:1979;309-333.
4. Prosser J.I. Autotrophic nitrification in bacteria. Adv. Microbiol. Physiol. 30:1989;125-181.
5. De Boer W., Klein-Gunnewiek P.J.A., Troelstra S.R. Nitrification in Dutch heathland soils. II. Characteristics of nitrate production. Plant Soil. 127:1990;193-200.
6. Bakker, J.P. (1989) Geobotany 14: Nature Management by Grazing and Cutting. Kluwer, Dordrecht.
7. Hassink, J.D. (1990) Nitrogen in grassland soils. In: Proceedings 13th General Meeting of the European Grassland Federation Vol. II (Gabornic, N. and Zimkova, M., Eds.), British Grassland Society, Reading, UK, pp. 25-32.
8. Olff, H. (1992) Consequences of changing nutrient supply rates for grassland vegetation I. Seasonal dynamics of nitrogen mineralization, biomass and tissue nutrient concentrations. In: On the Mechanisms of Vegetation Succession. PhD thesis, State University of Groningen.
9. Schmidt, E.L. and Belser, L.W. (1982) Nitrifying bacteria. In: Methods of Soil Analysis (Page, A.L., Miller, R.H. and Keeney, D.R., Eds.), Agronomy 9, Part 2, 2nd Edn. American Society of Agronomy, Madison, WI.
10. Batchelor S.E., Cooper M., Chabra S.R., Glover L.A., Stewart G.S.A.B., Williams P., Prosser J.I. Cell density-regulated recovery of starved biofilm populations of ammonium-oxidizing bacteria. Appl. Environ. Microbiol. 63:1997;2281-2286.
11. 3 availability. Appl. Environ. Microbiol. 63:1997;4588-4592.
12. Stein L.Y., Arp D.J. Ammonium limitation results in the loss of ammonium-oxidizing activity in Nitrosomonas europaea. Appl. Environ. Microbiol. 64:1998;1514-1521.
13. De Boer W., Klein Gunnewiek P.A., Laanbroek H.J. Ammonium-oxidation at low pH by a chemolithotrophic bacterium belonging to the genus Nitrosospira. Soil Biol. Biochem. 27:1995;127-132.
14. De Boer W., Tietema A., Klein Gunnewiek P.J.A., Laanbroek H.J. The chemolithotrophic ammonium-oxidizing community in a nitrogen-saturated acid forest soil in relation to pH-dependent nitrifying activity. Soil Biol. Biochem. 24:1992;229-234.
15. McCaig A.E., Embley T.M., Prosser J.I. Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol. Lett. 120:1994;363-368.
16. Stephen J.R., McCaig A.E., Smith Z., Prosser J.I., Embley T.M. Molecular diversity of soil and marine 16S rDNA sequences related to β-subgroup ammonia-oxidising bacteria. Appl. Environ. Microbiol. 62:1996;4147-4154.
17. Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J.I., Embley T.M., Woldendorp J.W. Analysis of β-proteobacteria ammonia-oxidizing bacteria in coastal sand dunes using denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S rDNA fragments. Appl. Environ. Microbiol. 63:1997;1489-1497.
18. Stephen J.R., Kowalchuk G.A., Bruns M.-A.V., McCaig A.E., Phillips C.J., Embley T.M., Prosser J.I. Analysis of β-subgroup ammonia oxidiser populations in soils by DGGE analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:1998;2958-2965.
19. Rotthauwe J.-H., Witzel K-P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:1997;4704-4712.
20. Hyman R.K., Wood P.M. Suicidal inactivation and labelling of ammonia mono-oxygenase by acetylene. Biochem. J. 27:1985;719-725.
21. 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. 139:1993;1147-1153.
22. Teske A., Elm E., Regan J.M., Toze S., Rittmann B.E., Stahl D.A. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176:1994;6623-6630.
23. Maidak B.L., Olsen G.J., Larsen N., Overbeek R., McCaughey M.J., Woese C.R. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:1997;109-111.
24. Speksnijder A.G.C.L., Kowalchuk G.A., Roest K., Laanbroek H.J. Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. System. Appl. Microbiol. 21:1998;321-330.
25. McCaig A.E., Phillips C.J., Stephen J.R., Kowalchuk G.A., Harvey M., Herbert R.A., Embley T.M., Prosser J.I. Nitrogen cycling and community structure of β-subgroup ammonia oxidising bacteria within polluted, marine fish-farm sediments. Appl. Environ. Microbiol. 65:1999;213-220.
26. Kowalchuk, G.A., Stienstra, A.W., Heilig, G.H.J., Stephen, J.R. and Woldendorp, J.W. (1999) Changes in the community structure of ammonia-oxidising bacteria during secondary succession of calcareous grasslands. Environ. Microbiol., in press.
27. Bruns M.A., Stephen J.R., Kowalchuk G.A., Prosser J.I., Paul E.A. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in never-tilled, tilled, and successional soils. Appl. Environ. Microbiol. 65:1999;2994-3000.
28. Stephen J.R., Chang Y.-J., Macnaughton S.J., Kowalchuk G.A., Leung K.T., Flemming C.A., White D.C. 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. 65:1999;95-101.
29. Carcia-delgado M., Gonzalez-Navarro C.J., Napal M.C., Baldonado C., Vizmanos J.L., Gullon A. Higher sensitivity of denaturing gradient gel electrophoresis than sequencing in the detection of mutations in DNA from tumor samples. Biotechniques. 24:1998;72-76.
30. Hastings R.C., Ceccherini M.T., Miclaus N., Saunders J.R., Bazzicalupo M., McCarthy A.J. Direct molecular biological analysis of ammonia oxidising bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23:1997;45-54.
31. Kowalchuk G.A., Bodelier P.L.E., Heilig G.H.J., Stephen J.R., Laanbroek H.J. Community analysis of ammonia-oxidising bacteria, in relation to oxygen-availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol. Ecol. 27:1998;339-350.
32. 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. 62:1996;625-630.
33. Rochelle P.A., Cragg B.A., Fry J.C., Parkes R.J., Weightman A.J. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecol. 15:1994;215-226.
34. Gillian D.C., Speksnijder A.G.C.L., Zwart G., De Ridder C. Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, Bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 64:1998;3464-3472.
35. Munro P.E. Inhibition of nitrifiers by grass root extracts. J. Appl. Ecol. 3:1966;229-231.
36. Rice, E.L. (1984) Natural ecosystems: Allelopathy and old-field or urban succession. In: Allelopathy (Rice, E.L., Ed.) Series Physiological Ecology, 2nd Edn., pp. 206-231. Academic Press, New York.
37. Bramley R.G.V., White R.E. The effect of pH, liming, moisture and temperature on the activity of nitrifiers in a soil under pasture. Austr. J. Soil Res. 27:1989;711-724.