Nitrogen cycling and community structure of proteobacterial β-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments

Applied and Environmental Microbiology

Volumn 65, Issue 1, 1999, Pages 213-220

  McCaig, Allison E ^a   Phillips, Carol J ^b,c   Stephen, John R ^a,d,f   Kowalchuk, George A ^e   Martyn Harvey, S ^b   Herbert, Rodney A ^c   Martin Embley, T ^d   Prosser, James I ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b SCOTTISH MARINE INSTITUTE   (United Kingdom)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

^d DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^e NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^f UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; NITROGEN;

BACTERIUM; COMMUNITY STRUCTURE; MARICULTURE; NITROGEN CYCLE; POLLUTION EFFECT; SEDIMENT;

ARTICLE; DENITRIFICATION; FOOD INDUSTRY; GEL ELECTROPHORESIS; NITRIFICATION; NITROBACTER; NITROGEN FIXATION; NITROSOMONAS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; SEDIMENT; SEQUENCE ANALYSIS; WATER POLLUTION;

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; NEGIBACTERIA; NITROBACTER; NITROSOMONADALES; NITROSOMONAS; PROTEOBACTERIA;

EID: 0032954211     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.1.213-220.1999     Document Type: Article

References (44)

1. Alexander, M. 1965. Denitrifying bacteria, p. 1484-1486. In C. A. Black (ed.), Methods of soil analysis, vol. 9. American Society of Agronomy. Madison, Wis.
2. Alexander, M., and F. E. Clark. 1965. Nitrifying bacteria, p. 1477-1483. In C. A. Black (ed.), Methods of soil analysis, vol. 9. American Society of Agronomy, Madison, Wis.
3. +, and CO oxidation by methanotrophs and nitrifiers. Microbiol. Rev. 53:68-84.
4. Bianchi, M., P. Bonin, and F. Feliatra. 1994. Bacterial nitrification and denitrification rates in the Rhone River plume (northwestern Mediterranean Sea). Mar. Ecol. Prog. Ser. 103:197-202.
5. Blackburn, T. H., and N. D. Blackburn. 1992. Model of nitrification and denitrification in marine sediments. FEMS Microbiol. Lett. 100:517-522.
6. Brosius, J., T. L. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. 3. Mol. Biol. 14:107-127.
7. Byers, S. C., E. L. Mills, and P. L. Stewart. 1978. Measurements of the physical and chemical environments, p. 30-58. In N. A. Holme and A. D. McIntyre (ed.), Methods for the study of marine benthos. Blackwell Scientific, Oxford, United Kingdom.
8. Caffrey, J. M., N. P. Sloth, H. F. Kaspar, and T. H. Blackburn. 1993. Effect of organic loading on nitrification and denitrification in a marine sediment microcosm. FEMS Microbiol. Ecol. 12:159-167.
9. Dugdale, R. C. 1967. Nutrient limitation in the sea: dynamics, identification and significance. Limnol. Oceanogr. 12:685-695.
10. Felsenstein, J. 1993. PHYLIP: phytogeny inference package. University of Washington, Seattle.
11. Hall, P. O. J., O. Holby, S. Kollberg, and M.-O. Samuelsson. 1992. Chemical fluxes and mass balances in a marine fish cage farm. IV. Nitrogen. Mar. Ecol. Prog. Ser. 89:81-91.
12. 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.
13. Hynes, R. K., and R. Knowles. 1983. Inhibition of chemoautotrophic nitrification by sodium chlorate and sodium chlorite: a reexamination. Appl. Environ. Microbiol. 45:1178-1182.
14. Johnsen, R. I., O. Grahl-Nielsen, and B. T. Lunestad. 1993. Environmental distribution of organic waste from a marine fish farm. Aquaculture 118:229-244.
15. Johnstone, B. H., and R. D. Jones. 1988. Effects of light and CO on the survival of a marine ammonia-oxidizing bacterium during energy source deprivation. Appl. Environ. Microbiol. 54:2890-2893.
16. Jones, R. D., and M. A. Hood. 1980. Effects of temperature, pH, salinity, and inorganic nitrogen on the rate of ammonium oxidation by nitrifiers isolated from wetland environments. Microb. Ecol. 6:339-347.
17. Jones, R. D., and R. Y. Morita. 1985. Survival of a marine ammonium-oxidiser under energy-source deprivation. Mar. Ecol. Prog. Ser. 26:175-179.
18. Jorgensen, K. S., and N.-P. Revsbech. 1985. Diffusive boundary layers and the oxygen uptake of sediments and detritus. Limnol. Oceanogr. 30:111-122.
19. 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.
20. Juliette, L. Y., M. R. Hyman, and D. J. Arp. 1993. Inhibition of ammonia oxidation in Nitrosomonas europaea by sulfur compounds: thioethers are oxidized to sulfoxides by ammonia monooxygenase. Appl. Environ. Microbiol. 59:3718-3727.
21. Kaspar, H. F., G. H. Hall, and A. J. Holland. 1988. Effects of sea cage salmon farming on sediment nitrification and dissimilatory nitrate reductions. Aquaculture 70:333-344.
22. Keener, W. K., and D. J. Arp. 1994. Transformations of aromatic compounds by Nitrosomonas europaea. Appl. Environ. Microbiol. 60:1914-1920.
23. Kowalchuk, G. A., J. R. Stephen, W. De Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorf. 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. Laanbroek, H. J., P. L. E. Bodelier, and S. Gerards. 1994. Oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter hamburgensis in mixed continuous cultures at different oxygen concentrations. Arch. Microbiol. 161:156-162.
25. MacFarlane, G. T., and R. A. Herbert. 1984. Dissimilatory nitrate reduction and nitrification in estuarine sediments. J. Gen. Microbiol. 130:2301-2308.
26. Maidak, B. L., N. Larsen, J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The ribosomal database project. Nucleic Acids Res. 22:3485-3487.
27. 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.
28. Meincke, M., E. Bock, D. Kastrauand, and P. M. H. Kroneck. 1992. Nitrite oxidoreductase from Nitrobacter hamburgensis - redox centers and their catalytic role. Arch. Microbiol. 158:127-131.
29. 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.
30. Parsons, T. R., Y. Maita, and C. M. Lalli. 1984. A manual of chemical and biological methods for seawater analysis. Pergamon Press, Oxford, United Kingdom.
31. Raymond, N., P. Bonin, and J.-C. Bertrand. 1992. Comparison of methods for measuring denitrifying activity in marine sediments from the western Mediterranean coast. Oceanol. Acta 15:137-143.
32. Rowe, R., R. Todd, and J. Waide. 1977. Microtechnique for most-probable-number analysis. Appl. Environ. Microbiol. 33:675-680.
33. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
34. Schmidt, I., and E. Bock. 1997. Anaerobic ammonia oxidation with nitrogen dioxide by Nitrosomonas eutropha. Arch. Microbiol. 167:106-111.
35. Sheffield, V. C., D. R. Cox, L. S. Lerman, and R. M. Myers. 1989. Attachment of a 40-base pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86:232-236.
36. Sloth, N. P., H. Blackburn, L. H. Hansen, N. Risgaard-Petersen, and B. A. Lomstein. 1995. Nitrogen cycling in sediments with different organic loading. Mar. Ecol. Prog. Ser. 116:163-170.
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. Sundermeyer-Klinger, H., W. Meyer, B. Warninghoff, and E. Bock. 1984. Membrane-bound nitrite oxidoreductase of Nitrobacter - evidence for a nitrate reductase system. Arch. Microbiol. 140:153-158.
40. Utaker, J. B., L. Bakken, Q. Q. Jiang, and I. F. Nes. 1996. Phylogenetic analysis of seven new isolates of ammonia-oxidising bacteria based on 16S rRNA gene sequences. Syst. Appl. Microbiol. 18:549-559.
41. Warner, G. F., and J. C. J. Domaniewski. 1993. Fish farming and the environment. Biologist 40:202-205.
42. Watson, S. W., E. Bock, H. Harms, H.-P. Koops, and A. B. Hooper. 1989. Nitrifying bacteria, p. 1808-1834. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins Co., Baltimore, Md.
43. Woese, C. R., W. G. Weisburg, B. J. Paster, C. M. Hahn, R. S. Tanner, N. R. Krieg, H.-P. Koops, H. Harms, and E. Stackebrandt. 1984. The phylogeny of the purple bacteria: the beta-subdivision. Syst. Appl. Microbiol. 5:327-336.
44. Woese, C. R., W. G. Weisburg, C. M. Hahn, B. J. Paster, L. B. Zahlen, B. J. Lewis, T. J. Macke, W. Ludwig, and E. Stackebrandt. 1985. The phylogeny of the purple bacteria: the gamma-subdivision. Syst. Appl. Microbiol. 6:25-33.