Surface attachment of ammonia-oxidizing bacteria in soil

Microbial Ecology

Volumn 39, Issue 3, 2000, Pages 222-235

  Aakra, Å ^a   Hesselsoe M ^b,c   Bakken, L R ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c AALBORG UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; BACTERIUM ADHERENCE; BACTERIUM DETECTION; CELL SURFACE; DENSITY GRADIENT CENTRIFUGATION; OXIDATION; PARTICLE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIMER DNA; SOIL; UREA;

NITROSOSPIRA;

EID: 0033924053     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (53)

1. Aakra Å, Utåker JB, Nes IF (1999) RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: A phylogenetic approach. Int J Syst Bacteriol 49:123-130
2. Alexander M (1965) Nitrification. In: Bartolomew W, Clark FE (eds) Soil Nitrogen. American Society of Agronomy, Madison, WI, pp 307-343
3. Allison SM, Prosser JI (1993) Ammonia oxidation at low pH by attached populations of nitrifying bacteria. Soil Biol Biochem 25:935-941
4. Altschul SF, Gish W, Miller W, Myers EW, Lipmann DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-441
5. Amann R, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microb Rev 59:143-169
6. Bakken LR (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49:1482-1487
7. Bakken LR (1997) Culturable and unculturable bacteria in soil. In: van Elsas JD, Wellington EMH, Trevors JT (eds) Modern Soil Microbiology. Marcel Dekker, New York, pp 47-61
8. Bakken LR, Lindahl V (1995) Recovery of bacterial cells from soil. In: Trevors JT, van Elsas JD (eds) Nucleic Acids in the Environment. Methods and Applications. Springer Verlag, Berlin, pp 9-27
9. Batchelor SE, Cooper M, Chhabra SR, Glover LA, Stewart GSAB, Williams P, Prosser JI (1997) Cell density regulated recovery of starved biofilm populations of ammonia-oxidizing bacteria. Appl Environ Microbiol 63:2281-2286
10. Belser LW, Mays EL (1980) Specific inhibition of nitrite oxidation by chlorate and its use in assessing nitrification in soil and sediments. Appl Environ Microbiol 39:505-510
11. Berg P, Rosswall T (1985) Ammonium oxidizer number, potential and actual oxidation rates in two Swedish arable soils. Biol Fert Soils 1:131-140
12. Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801-4805
13. 2O. Appl Environ Microbiol 54:1409-1413
14. Collins CM, D'Orazio EF (1993) Bacterial ureases: Structure, regulation of expression and role in pathogenesis. Mol Microbiol 9:907-913
15. Donaldson JM, Henderson GS (1989) A dilute medium to determine population size of ammonium oxidizers in forest soils. Soil Sci Soc Am J 53:1608-1611
16. Dorsch M, Stackebrandt E (1992) Some modifications in the procedure of direct sequencing of PCR amplified 16S-rDNA. J Microbiol Meth 16:271-279
17. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791
18. Felsenstein J (1993) PHYLIP (Phylogeny Intertace Package), Version 3.5c, Distributed by the author, Department of Genetics, University of Washington, Seattle
19. Head IM, Hiorns WD, Embley TM, McCarthy AJ, Saunders JR (1993) The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequenses. J Gen Microbiol 139:1147-1153
20. Højberg O, Binnerup SJ, Sørensen J (1997) Growth of silicone-immobilized bacteria on polycarbonate membrane filters, a technique to study microcolony formation under anaerobic conditions. Appl Environ Microbiol 63:2920-2924
21. Jiang QQ, Bakken LR (1999) Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiol Ecol 30:171-186
22. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:120
23. Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM, Woldendorp JW (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
24. Lindahl V, Bakken LR (1995) Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol Ecol 16:135-142
25. McCaig AE, Embley TM, Prosser JI (1994) Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett 120:363-368
26. Mobarry BK, Wagner M, Urbain V, Rittmann BE, Stahl DA (1996) Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl Environ Microbiol 62:2156-2162
27. Mobarry BK, Wagner M, Urbain V, Rittmann BE, Stahl DA (1997) Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria (erratum). Appl Environ Microbiol 63:815
28. Page RDM (1996) TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
29. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63-98
30. Pearson WR, Lipmann DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85:2444-2448
31. Phillips CJ, Smith Z, Embley TM, Prosser JI (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
32. Pommereninger-Röser A, Rath G, Koops HP (1999) Phylogenetic diversity within the genus Nitrosomonas. System Appl Microbiol 19:344-351
33. Priemé A, Sitaula JIB, Klemedtsson ÅK, Bakken LR (1996) Extraction of methane-oxidizing bacteria from soil particles. FEMS Microbiol Ecol 21:59-68
34. Prosser JI (1989) Autotrophic nitrification in bacteria. Adv Microb Phys 30:125-177
35. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
36. Sarathchandra SU (1979) A simplified method for estimating ammonium oxidising bacteria. Plant Soil 52:305-309
37. 4) by widebore capillary GC. J Environ Quality 21:493-496
38. Stackebrandt E, Charfreitag O (1990) Partial 16S rRNA primary structure of five Actinornyces species: Phylogenetic implications and development of an Actinornyces israelii specific oligonucleotide probe. J Gen Microbiol 136:37-43
39. Stark JM, Firestone MK (1995) Mechanisms for soil moisture effects on activity of nitrifying bacteria. Appl Environ Microbiol 61:218-221
40. Stehr G, Zörner S, Böttcher B, Koops HP (1995) Exopolymers: An ecological characteristic of a floc-attached, ammonia-oxidizing bacterium. Microb Ecol 30:115-126
41. Stephen JR, Chang YJ, Macnaughton SJ, Kowalchuk GA, Leung KT, Flemming CA, White DC (1999) Effects 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
42. Stephen JR, Kowalchuk GA, Bruns MV, McCaig AE, Phillips CJ, Embley TM, Prosser JI (1998) Analysis of the β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl Environ Microbiol 64:2958-2965
43. Stephen JR, McCaig AE, Smith Z, Prosser JI, Embley TM (1996) Molecular diversity of soil and marine 16S rRNA gene sequenses related to β-subgroup ammonia-oxidizing bacteria. Appl Environ Microbiol 62:4147-4154
44. Tappe W, Laverman A, Bohland M, Braster M, Ritterhaus S, Groeneweg J, van Verseveld HW (1999) Maintenance energy demand and starvation recovery dynamics of Nitrosomonas europaea and Nitrobacter winogradskyi cultivated in retentostat with complete biomass retention. Appl Environ Microbiol 65:2471-2477
45. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive mutiple sequence alignment through sequence weighting, positions-specific gap penalities and weight matrix choise. Nucleic Acids Res 22:4673-4680
46. Utåker JB, Bakken LR, Jiang QQ, Nes IF (1995) Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. System Appl Microbiol 18:549-559
47. Utåker JB, Nes IF (1998) A qualitative evaluation of the published oligonucleotides specific for the 16S rRNA gene sequences of the ammonia-oxidizing bacteria. System Appl Microbiol 21:72-88
48. Verhagen FJM, Duyts H, Laanbroek HJ (1993) Effects of grazing by flagellates on competition for ammonium between nitrifying and heterotrophic bacteria in soil columns. Appl Environ Microbiol 59:2099-2106
49. Verhagen FJM, Hageman PEJ, Woldendorp JW, Laanbroek HJ (1994) Competion for ammonium between nitrifying bacteria and plant roots in soil in pots; effects of grazing by flagellates and fertilization. Soil Biol Biochem 26:89-96
50. Wagner M, Rath G, Amann R, Koops HP, Schleifer KH (1995) In situ identification of ammonia-oxidizing bacteria. System Appl Microbiol 18:251-264
51. Watson SW, Bock E, Harms H, Koops HP, Hooper AB (1989) Nitrifying bacteria. In: Murray RGE, Brenner DJ, Bryant MP, Holt JG, Krieg NR, Moulder JW, Phenning N, Sneath PHA, Stanley JT, Williams S (eds) Bergey's Manual of Systematic Bacteriology. The Williams & Wilkins Co, Baltimore, pp 1808-1834
52. Woese CR, Weisburg WG, Paster BJ, Hahn CM, Tanner RS, Krieg NR, Koops HP, Harms H, Stackebrandt E (1984) The phylogeny of purple bacteria: The beta subdivision. System Appl Microbiol 5:327-336
53. Woomer PL (1994) Most probable number counts. In: Weaver RW, Angle JS, Bottomley PS (eds) Methods of Soil Analysis, Part 2: Microbiological and Biochemical Properties. Soil Science Society of America, Madison, WI, pp 59-79