Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals

Applied and Environmental Microbiology

Volumn 74, Issue 17, 2008, Pages 5475-5482

  Park, Sunhwa ^a   Ely, Roger L ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BATCH REACTORS; CADMIUM; COPPER; DENITRIFICATION; HEAVY METALS; MERCURY (METAL); NITRIFICATION; OXIDATION; WASTEWATER RECLAMATION; WASTEWATER TREATMENT; WATER TREATMENT; WATER TREATMENT PLANTS;

NITROSOMONAS EUROPAEA; QUASI-STEADY STATES;

CHEMICALS REMOVAL (WATER TREATMENT);

CADMIUM CHLORIDE; COPPER CHLORIDE; HEAVY METAL; MERCURIC CHLORIDE; MERCURY (II) REDUCTASE; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

BACTERIUM; HEAVY METAL; INHIBITION; MONITORING; NITRIFICATION; PROTEOMICS; STRESS; WASTEWATER; WATER TREATMENT;

ARTICLE; BACTERIAL GENE; BATCH REACTOR; DOWN REGULATION; GENE FUNCTION; GENETIC TRANSCRIPTION; NITRIFICATION; NITROSOMONAS EUROPAEA; OXIDATION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEOMICS; STRESS; UPREGULATION;

AMMONIA; CADMIUM CHLORIDE; COPPER; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MERCURIC CHLORIDE; NITRITES; NITROSOMONAS EUROPAEA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATION-REDUCTION; OXIDOREDUCTASES; OXYGEN CONSUMPTION; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TRANSCRIPTION, GENETIC; UP-REGULATION;

NITROSOMONAS EUROPAEA;

EID: 50949106204     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00500-08     Document Type: Article

References (48)

1. Arp, D. J., L. A. Sayavedra-Soto, and N. G. Hommes. 2002. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch. Microbiol. 178:250-255.
2. Barkay, T., S. M. Miller, and A. O. Summers. 2003. Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol. Rev. 27:355-384.
3. Beaumont, H. J., N. G. Hommes, L. A. Sayavedra-Soto, D. J. Arp, D. M. Arciero, A. B. Hooper, H. V. Westerhoff, and R. J. van Spanning. 2002. Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite. J. Bacteriol. 184:2557-2560.
4. Benmossa, H., G. Martin, Y. Richard, and A. Leprince. 1986. Inhibition of nitrification by heavy metal cations. Water Res. 20:1333-1339.
5. Braam, F., and A. Klapwijk. 1981. Effect of copper on nitrification in activated sludge. Water Res. 15:1093-1098.
6. Celis, J. E., M. Kruhoffer, I. Gromova, C. Frederiksen, M. Ostergaard, T. Thykjaer, P. Gromov, J. Yu, H. Palsdottir, N. Magnusson, and T. F. Orntoft. 2000. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and protcomics. FEBS Lett. 480:2-16.
7. Chandran, K., and N. G. Love. 2008. Physiological state, growth mode, and oxidative stress play a role in Cd(II)-mediated inhibition of Nitrosomonas europaea 19718. Appl. Environ. Microbiol. 74:2447-2453.
8. Crosa, J. H. 1997. Signal transduction and transcriptional and posttranscriptional control of iron-regulated genes in bacteria. Microbiol. Mol. Biol. Rev. 61:319-336.
9. Dick, G. J., J. W. Torpey, T. J. Beveridge, and B. M. Tebo. 2008. Direct identification of a bacterial manganese(II) oxidase, the multicopper oxidase MnxG, from spores of several different marine Bacillus species. Appl. Environ. Microbiol. 74:1527-1534.
10. Ely, R. L., M. R. Hyman, D. J. Arp, R. B. Guenther, and K. J. Williamson. 1995. A cometabolic kinetics model incorporating enzyme inhibition, inactivation, and recovery. 2: Trichloroethylene degradation experiments. Biotechnol. Bioeng. 46:232-245.
11. Ensign, S. A., M. R. Hyman, and D. J. Arp. 1993. In vitro activation of ammonia monooxygenase from Nitrosomonas europaea by copper. J. Bacteriol. 175:1971-1980.
12. Ferianc, P., A. Farewell, and T. Nystrom. 1998. The cadmium-stress stimulon of Escherichia coli K-12. Microbiology 144:1045-1050.
13. Grizot, S., and S. K. Buchanan. 2004. Structure of the OmpA-like domain of RmpM from Neisseria meningitidis. Mol. Microbiol. 51:1027-1037.
14. m: effects of pH and temperature. Water Res. 28:2561-2566.
15. Gvakharia, B. O., E. A. Permina, M. S. Gelfand, P. J. Bottomley, L. A. Sayavedra-Soto, and D. J. Arp. 2007. Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane. Appl. Environ. Microbiol. 73:3440-3445.
16. 2O dynamics. Soil Biol. Biochem. 34:1181-1190.
17. Horn, J. M., M. Brunke, W. D. Deckwer, and K. N. Timmis. 1994. Pseudomonas putida strains which constitutively overexpress mercury resistance for biodetoxification of organomercurial pollutants. Appl. Environ. Microbiol. 60:357-362.
18. Hsieh, J., A. J. Andrews, and C. A. Fierke. 2004. Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P. Biopolymers 73:79-89.
19. Hu, P., E. L. Brodie, Y. Suzuki, H. H. McAdams, and G. L. Andersen. 2005. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J. Bacteriol. 187:8437-8449.
20. Hu, Z., K. Chandran, D. Grasso, and B. F. Smets. 2004. Comparison of nitrification inhibition by metals in batch and continuous flow reactors. Water Res. 38:3949-3959.
21. Hu, Z., K. Chandran, D. Grasso, and B. F. Smets. 2002. Effect of nickel and cadmium speciation on nitrification inhibition. Environ. Sci. Technol. 36:3074-3078.
22. Hyman, M. R., and D. J. Arp. 1995. Effects of ammonia on the de novo synthesis of polypeptides in cells of Nitrosomonas europaea denied ammonia as an energy source. J. Bacteriol. 177:4974-4979.
23. Hyman, M. R., S. A. Russell, R. L. Ely, K. J. Williamson, and D. J. Arp. 1995. Inhibition, inactivation, and recovery of ammonia-oxidizing activity in cometabolism of trichloroethylene by Nitrosomonas europaea. Appl. Environ. Microbiol. 61:1480-1487.
24. Imlay, J. A., and S. Linn. 1986. Bimodal pattern of killing of DNA-repair-defective or anoxically grown Escherichia coli by hydrogen peroxide. J. Bacteriol. 166:519-527.
25. Isaacs, F. J., D. J. Dwyer, C. Ding, D. D. Pervouchine, C. R. Cantor, and J. J. Collins. 2004. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22:841-847.
26. Johnson, G. D., and J. S. Bond. 1999. Cell-associated metalloproteinases. Birkhäuser Verlag, Basel, Switzerland.
27. Juliastuti, S. R., J. Baeyens, C. Creemers, D. Bixio, and E. Lodewyckx. 2003. The inhibitory effects of heavy metals and organic compounds on the net maximum specific growth rate of the autotrophic biomass in activated sludge. J. Hazard Mater. 100:271-283.
28. Koller, L. D. 1998. Immunotoxicology of environmental and occupational metals. CRC Press, Boca Raton, FL.
29. Le Roch, K. G., J. R. Johnson, L. Florens, Y. Zhou, A. Santrosyan, M. Grainger, S. F. Yan, K. C. Williamson, A. A. Holder, D. J. Carucci, J. R. Yates III, and E. A. Winzeler. 2004. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 14:2308-2318.
30. Leung, W. C., M.-F. Wong, H. Chua, W. Lo, P. H. F. Yu, and C. K. Leung. 2000. Removal and recovery of heavy metals by bacteria isolated from activated sludge treating industrial effluents and municipal wastewater. Water Sci. Technol. 41:233-240.
31. Liebert, C. A., R. M. Hall, and A. O. Summers. 1999. Transposon Tn21, flagship of the floating genome. Microbiol. Mol. Biol. Rev. 63:507-522.
32. Lim, H., K. Kim, D. Han, J. Oh, and Y. Kim. 2007. Crystal structure of TTC0263, a thermophilic TPR protein from Thermus thermophilus HB27. Mol. Cells 24:27-36.
33. Madoni, P., D. Davoli, and L. Guglielmi. 1999. Response of SOUR and AUR to heavy metal contamination in activated sludge. Water Res. 33:2459-2464.
34. Mindlin, S., G. Kholodii, Z. Gorlenko, S. Minakhina, L. Minakhin, E. Kalyaeva, A. Kopteva, M. Petrova, O. Yurieva, and V. Nikiforov. 2001. Mercury resistance transposons of gram-negative environmental bacteria and their classification. Res. Microbiol. 152:811-822.
35. Mindlin, S., L. Minakhin, M. Petrova, G. Kholodii, S. Minakhina, Z. Gorlenko, and V. Nikiforov. 2005. Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene. Res. Microbiol. 156:994-1004.
36. Nazaret, S., W. H. Jeffrey, E. Saouter, R. Von Haven, and T. Barkay, 1994. merA gene expression in aquatic environments measured by mRNA production and Hg(II) volatilization. Appl. Environ. Microbiol. 60:4059-4065.
37. Nies, D. H. 1999. Microbial heavy-metal resistance. Appl. Microbiol. Biotechnol. 51:730-750.
38. Park, S., and R. L. Ely. 2008. Genome-wide transcriptional responses of Nitrosomonas europaea to zinc. Arch. Microbiol. 189:541-548.
39. Peirson, S. N., J. N. Butler, and R. G. Foster. 2003. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res. 31:e73.
40. Principi, P., F. Villa, M. Bernasconi, and E. Zanardini. 2006. Metal toxicity in municipal wastewater activated sludge investigated by multivariate analysis and in situ hybridization. Water Res. 40:99-106.
41. Radniecki, T. S., and R. L. Ely. 2008. Zinc chloride inhibition of Nitrosococcus mobilis. Biotechnol. Bioeng. 99:1085-1095.
42. Schmidt, I., P. J. Steenbakkers, H. J. op den Camp, K. Schmidt, and M. S. Jetten. 2004. Physiologic and proteomic evidence for a role of nitric oxide in biofilm formation by Nitrosomonas europaea and other ammonia oxidizers. J. Bacteriol. 186:2781-2788.
43. +) reduces denitrification and induces enrichment of novel nirK genotypes in soil. FEMS Microbiol. Lett. 270:189-194.
44. U.S. Environmental Protection Agency. 1993. Process design manual: nitrogen control. Report 625/R-93/010. U.S. Environmental Protection Agency, Washington, DC.
45. Wang, A., and D. E. Crowley. 2005. Global gene expression responses to cadmium toxicity in Escherichia coli. J. Bacteriol. 187:3259-3266.
46. Watson, S. W., F. W. Valois, and J. B. Waterbury. 1981. The family Nitrobacteraceae, p. 1005-1022. In M. P. Starr, J. Stolp, H. G. Truper, A. Balows, and H. G. Schlegel (ed.), The prokaryotes: a handbook on habitats, isolation, and identification of bacteria. Springer-Verlag, New York, NY.
47. Wei, X., L. A. Sayavedra-Soto, and D. J. Arp. 2004. The transcription of the cbb operon in Nitrosomonas europaea. Microbiology 150:1869-1879.
48. Wei, X., T. Yan, N. G. Hommes, X. Liu, L. Wu, C. McAlvin, M. G. Klotz, L. A. Sayavedra-Soto, J. Zhou, and D. J. Arp. 2006. Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate. FEMS Microbiol. Lett. 257:76-83.