Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

Applied and Environmental Microbiology

Volumn 67, Issue 8, 2001, Pages 3426-3433

  Oved, Tamar ^a,b   Shaviv, Avi ^b   Goldrath, Tal ^b   Mandelbaum, Raphi T ^a   Minz, Dror ^a  

^a VOLCANI CENTER   (Israel)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; AMMONIA MONOOXYGENASE; OXIDOREDUCTASE;

AGRICULTURE; ARTICLE; BACTERIUM; CLASSIFICATION; ECOSYSTEM; ELECTROPHORESIS; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NITROSOMONAS; OXIDATION REDUCTION REACTION; POLYMERASE CHAIN REACTION; SOIL; WATER POLLUTION;

AGRICULTURE; AMMONIA; BACTERIA; ECOSYSTEM; ELECTROPHORESIS; MOLECULAR SEQUENCE DATA; NITROSOMONAS; OXIDATION-REDUCTION; OXIDOREDUCTASES; POLYMERASE CHAIN REACTION; SOIL; SOIL MICROBIOLOGY; WATER POLLUTION;

EID: 0035432486     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.8.3426-3433.2001     Document Type: Article

References (36)

1. Aakra, A., J. B. Utaker, and I. F. Nes. 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. Avnimelech, Y., and R. Wallach. 1991. Irrigation with treated effluent. Special report supported by the Ministries of Environment and Agriculture (Hebrew). Technion, Haifa, Israel.
3. Boer, W. D., H. Duyts, and H. J. Laanbroek. 1989. Urea stimulated autotrophic nitrification in suspensions of fertilized acid heath soil. Soil Biol. Biochem. 21:349-354.
4. Bremner, J. M., and C. S. Mulvaney. 1982. Nitrogen - total, p. 595-622. In A. L. Page, R. H. Miller, and D. R. Keeney (ed.), Methods of soil analysis, pt. 2, 2nd ed. American Society of Agronomy and Soil Science Society of America, Madison. Wis.
5. Bruns, M. A., J. R. Stephen, G. A. Kowalchuk, J. I. Prosser, and E. A. Paul. 1999. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled and successional soils. Appl. Environ. Microbiol. 65:2994-3000.
6. Hastings, R. C., M. T. Ceccherini, N. Micalus, J. R. Saunders, M. Bazzicalupo, and A. J. McCarthy. 1997. Direct molecular biological analysis of ammonia oxidizing bacteria population in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23:45-54.
7. Head, I. M., W. D. Hiorns, T. M. Embley, A. J. McCarthy, and J. R. Saunders. 1993. The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J. Gen. Microbiol. 139:1147-1153.
8. Horz, H. P., J. H. Rotthauwe, T. Lukow, and W. Liesack. 2000. Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J. Microbiol. Methods 39:197-204.
9. Jetten, M. S., S. Logemann, G. Muyzer, L. A. Robertson, S. de Vries, M. C. van Loosdrecht, and J. G. Kuenen. 1997. Novel principles in the microbial conversion of nitrogen compounds. Antonie Leeuwenhoek 71:75-93.
10. Koops, H. P., B. Boetteher, U. C. Moeller, R. A. Pommerening, and G. Stehr. 1991. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis, new species, Nitrosomonas ureae. new species, Nitrosomonas aestuarii, new species. Nitrosomonas marina, new species, Nitrosomonas nitrosa, new species, Nitrosomonas eutropha, new species, Nitrosomonas oligotropha, new species and Nitrosomonas halophila, new species. J. Gen. Microbiol. 137:1689-1700.
11. Koops, H. P., and U. C. Moller. 1992. The lithotrophic ammonia-oxidizing bacteria, p. 2625-2637. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer-Verlag, New York, N.Y.
12. Kowalchuk, G. A., P. L. E. Bodelier, G. H. J. Heilig, J. R. Stephen, and H. J. Laanbroek. 1998. Community analysis of ammonia-oxidizing bacteria, in relation to oxygen availability in soil and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridization. FEMS Microbiol. Ecol. 27:339-350.
13. Kowalchuk, G. A., S. Gerards, and J. W. Woldendorp. 1997. Detection and characterization of fungal infections of Anunophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl. Environ. Microbiol. 63:3858-3865.
14. Kowalchuk, G. A., Z. S. Naoumenko, P. J. L. 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.
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 beta 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. 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 beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl. Environ. Microbiol. 65:213-220.
17. Mendum, T. A., R. E. Sockett, and P. R. Hirsch. 1999. Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the beta subdivision of the class Proteobacteria in arable soils to nitrogen fertilizer. Appl. Environ. Microbiol. 65:4155-4162.
18. 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.
19. Muyzer, G., S. Hottentrager, A. Teske, and C. Wawer. 1996. Denaturing gradient gel electrophoresis of PCR-amplified 16S-rDNA - a new molecular approach to analyze the genetic diversity of mixed microbial communities, p. 1-23. In A. D. L. Akkermans, J. D. Van-Elsas, and F. J. De-Bruijn (ed.), Molecular microbial ecology manual, 1st ed. Kluwer Academic Publishers, London, United Kingdom.
20. Muyzer, G., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhock 73:127-141.
21. Paul, E. A., and F. E. Clark. 1989. Soil microbiology and biochemistry. Academic Press, Inc., San Diego, Calif.
22. Pettygrove, G. S., D. C. Davenport, and T. Asano. 1985. Introduction: California's reclaimed municipal wastewater resource, p. 1-14. In G. S. Pettygrove and T. Asano (ed.), Irrigation with reclaimed municipal wastewater - a guidance manual, 2nd ed. Lewis Publishers, Chelsea, Mich.
23. Pommerening, R. A., G. Rath, and H. P. Koops. 1996. Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19:344-351.
24. Princic, A., I. Mahne, F. Megusar, E. A. Paul, and J. M. Tiedje. 1998. Effects of pH and oxygen and ammonium concentrations on the community structure of nitrifying bacteria from wastewater. Appl. Environ. Microbiol. 64: 3584-3590.
25. Prosser, J. I. 1986. Nitrification. IRL Press, Oxford, United Kingdom.
26. Prosser, J. I. 1989. Autotrophic nitrification in bacteria. Adv. Microb. Physiol. 30:125-181.
27. Purhkold, U., A. Pommerening-Roser, S. Juretschko, M. C. Schmid, H. P. Koops, and M. Wagner. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implication for molecular diversity surveys. Appl. Environ. Microbiol. 66: 5368-5382.
28. 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 natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-4712.
29. Schramm, A., D. De Beer, M. Wagner, and R. Amann. 1998. Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environ. Microbiol. 64: 3480-3485.
30. 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 beta-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl. Environ. Microbiol. 65:95-101.
31. Stephen, J. R., G. A. Kowalchuk, M. A. Bruns, A. E. McCaig, C. J. Phillips, T. M. Embley, and J. I. Prosser. 1998. Analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:2958-2965.
32. 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 beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62: 4147-4154.
33. Thomas, T. L., R. W. Sheard, and J. R. Moyer. 1967. Comparison of conventional and automated procedures for nitrogen, phosphorus and potassium analysis of plant material using a single digestion. Agron. J. 59:240-250.
34. Wagner, M., G. Rath, R. Amann, H. P. Koops, and K. H. Schleifer. 1995. In situ identification of ammonia oxidizing bacteria. Syst. Appl. Microbiol. 18:251-264.
35. Wawer, C., M. S. Jetten, and G. Muyzer. 1997. Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples. Appl. Environ. Microbiol. 63:4360-4369.
36. Wawer, C., and G. Muyzer. 1995. Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments. Appl. Environ. Microbiol. 61:2203-2210.