Use of amoB as a new molecular marker for ammonia-oxidizing bacteria

Journal of Microbiological Methods

Volumn 57, Issue 1, 2004, Pages 69-78

  Calvó, Laia ^a   Garcia Gil, L Jesús ^a  

^a UNIVERSITY OF GIRONA   (Spain)

Author keywords

Ammonia monooxygenase; Ammonia oxidizing bacteria; Ammonium oxidizing bacteria; AMO; AOB; Methane oxidizing bacteria; MOB; Molecular marker; Nc; Nitrosococcus; Nitrosomonas; Nitrosospira; Nm; Nsp

Indexed keywords

AMINO ACID; AMMONIA; BACTERIAL DNA; MOLECULAR MARKER; UNSPECIFIC MONOOXYGENASE;

AMINO ACID SEQUENCE; AMMONIA OXIDIZING BACTERIA; ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL STRAIN; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA FLANKING REGION; GENE FUNCTION; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; NITROSOSPIRA; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, BACTERIAL; GENETIC MARKERS; MOLECULAR SEQUENCE DATA; NITROSOMONADACEAE; OXIDOREDUCTASES; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

AMOA; BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; NITROSOCOCCUS; NITROSOMONADALES; NITROSOMONAS; NITROSOSPIRA;

EID: 1542285223     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2003.11.019     Document Type: Article

References (54)

1. Aakra A., Utåker J.B., Nes I.F. 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. 49:1999;123-130.
2. Aakra A., Utåker J.B., Nes I.F., Bakken L.R. An evaluated improvement of the extinction dilution method for isolation of ammonia-oxidizing bacteria. J. Microbiol. Methods. 39:1999;23-31.
3. Aakra A., Utåker J.B., Pommerening-Röser A., Koops H.P., Nes I.F. Detailed phylogeny of ammonia-oxidizing bacteria determined by rDNA sequences and DNA homology values. Int. J. Syst. Evol. Microbiol. 51:2001;2021-2030.
4. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
5. Alzerreca J.J., Norton J.M., Klotz M.G. The amo operon in marine, ammonia-oxidizing gamma-proteobacteria. FEMS Microbiol. Lett. 180:1999;21-29.
6. Bergmann D.J., Hooper A.B. Sequence of the gene, amoB, for the 43-kDa polypeptide of ammonia monoxygenase of Nitrosomonas europaea. Biochem. Biophys. Res. Commun. 204:1994;759-762.
7. Bock E., Koops H.P., Harms H. Cell biology of nitrifying bacteria. Nitrification Spec. Publ. Soc. Gen. Microbiol. vol. 20:1986;17-38 IRL Press, Oxford.
8. Bothe H., Jost G., Schloter M., Ward B.B., Witzel K. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24:2000;673-690.
9. Calvó L., Vila X., Abella C.A., Garcia-Gil L.J. Use of the ammonia-oxidizing bacterial-specific phylogenetic probe Nso1225 as a primer for fingerprint analysis of ammonia-oxidizer communities. Appl. Microbiol. Biotechnol. 2003;. (in press).
10. Dayhoff M.O. Atlas of Protein Sequence and Structure. 1979;National Biomedical Research Foundation, Washington, DC.
11. Gilbert B., McDonald I.R., Finch R., Stafford G.P., Nielsen A.K., Murrell J.C. Molecular analysis of the pmo particulate methane monooxygenase. Operons from two type II methanotrophs. Appl. Environ. Microbiol. 66:2000;966-975.
12. 2O by nitrifying bacteria at reduced concentrations of oxygen. Appl. Environ. Microbiol. 40:1980;526-532.
13. Heiko A., Schmidt K.S., Vingron M., von Haeseler A. Strimmer K., von Haeseler Heiko A. TREE-PUZZLE. 1999;Schmidt Theoretical Bioinformatics Deutsches Krebsforschungszentrum DKFZ, Heidelberg, Germany.
14. Holmes A.J., Costello A., Lidstrom M.E., Murrell J.C. Evidence that particulate methane monooxygenase and ammonia monooxygenase might be evolutionary related. FEMS Microbiol. Lett. 132:1995;203-208.
15. Hommes N.G., Sayavedra-Soto L.A., Arp D.J. Mutagenesis and expression of amo, which codes for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 180:1998;3353-3359.
16. Hooper A.B. Biochemistry of the Nitrifying Lithoautotrophic Bacteria. 1989;239-265 Autotrophic Bacteria Science Tech. Publishers, Madison, Wisconsin.
17. 2-labeling studies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase. J. Biol. Chem. 267:1992;1534-1545.
18. Hyman M.R., Murton I.B., Arp D.J. Interaction of ammonia monooxygenase from Nitrosomonas europaea with alkanes, alkenes, and alkynes. Appl. Environ. Microbiol. 54:1988;3187-3190.
19. Jones R.D. Carbon monoxide and methane distribution and consumption in the photic zone of the Sargasso Sea. Deep-Sea Res. 38:1991;625-635.
20. Jones R.D., Morita R.Y. Carbon monoxide oxidation by chemolithotrophic ammonium oxidizers. Can. J. Microbiol. 29:1983;1545-1551.
21. Jones R.D., Morita R.Y. Carbon monoxide oxidation by Nitrosococcus oceani and Nitrosomonas europaea. Appl. Environ. Microbiol. 45:1983;401-410.
22. Juretschko S., Timmermann G., Schmid M., Schleifer K.H., Pommerening-Röser A., Koops H.P., Wagner M. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl. Environ. Microbiol. 64:1998;3042-3051.
23. Klotz M.G., Norton J.M. Multiple copies of ammonia monooxygenase amo. operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria. FEMS Microbiol. Lett. 168:1998;303-311.
24. Klotz M.G., Alzerreca J., Norton J.M. A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia oxidizing bacteria: a third member of the amo operon? FEMS Microbiol. Lett. 150:1997;65-73.
25. Koops H.P., Harms H. Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria. Arch. Microbiol. 141:1985;214-218.
26. Koops H.P., Böttcher B., Möller U.C., Pommerening-Röser A., Stehr G. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas comunis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov. and Nitrosomonas halophila sp. nov. J. Gen. Microbiol. 137:1991;1689-1699.
27. Kowalchuk G.A., Stienstra A.W., Heilig G.H., Stephen J.R., Woldendorp J.W. Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A The Netherlands. FEMS Microbiol. Ecol. 31:2000;207-215.
28. Kumar S., Tamura K., Jakobsen I.B., Nei M. MEGA2: Molecular Evolutionary Genetics Analysis software. 2001;Arizona State University, Tempe, AZ, USA.
29. Lane D.J. 16S/23S rRNA sequencing. Goodfellows S.A. Nucleic Acid Techniques in Bacterial Systematics. 1991;177-204 Wiley, Chichester.
30. 2O by soil nitrifying bacteria. Nature (Lond.). 294:1981;641-643.
31. McTavish H., Fuchs J.A., Hooper A.B. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 175:1993;2436-2444.
32. Nguyen H.H., Elliott S.J., Yip J.H., Chan S.I. The particulate methane monooxygenase from Methylococcus capsulatus Bath. is a novel copper-containing three-subunit enzyme. Isolation and characterization. J. Biol. Chem. 273:1998;7957-7966.
33. Nold S.C., Zhou J., Devol A.H., Tiedje J.M. Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria. Appl. Environ. Microbiol. 66:2000;4532-4535.
34. Norton J.M., Low J.M., Klotz M.G. The gene encoding ammonia monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 139:1996;181-188.
35. Norton J.M., Alzerreca J.J., Suwa Y., Klotz M.G. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch. Microbiol. 177:2002;139-149.
36. Olson R.J. 15N tracer studies of the primary nitrite maximum. J. Mar. Res. 39:1981;203-226.
37. Olson R.J. Differential photoinhibition of marine nitrifying bacteria: a possible mechanism for the formation of the primary nitrite maximum. J. Mar. Res. 39:1981;227-238.
38. Purkhold U., Pommerening-Röser A., Juretschko S., Schmid M.C., Koops H.P., Wagner M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66:2000;5368-5382.
39. Purkhold U., Wagner M., Timmermann G., Pommerening-Röser A., Koops H.P. 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53:2003;1485-1494.
40. Rotthauwe J.H., de Boer W., Liesack W. Comparative analysis of gene sequences encoding ammonia monooxygenase of Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71. FEMS Microbiol. Lett. 133:1995;131-135.
41. 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.
42. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
43. Sayavedra-Soto L.A., Hommes N.G., Alzerreca J.J., Arp D.J., Norton J.M., Klotz M.G. Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 167:1998;81-88.
44. Sinigalliano C.D., Kuhn D.N., Jones R.D. Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl. Environ. Microbiol. 61:1995;2702-2706.
45. Stephen J.R., McCaig A.E., Smith Z., Prosser J.I., Embley T.M. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62:1996;4147-4154.
46. Stolyar S., Costello A.M., Peeples T.L., Lidstrom M.E. Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology. 145:1999;1235-1244.
47. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic. Acids. Res. 22:1994;4673-4680.
48. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:1997;4876-4882.
49. Utåker J.B., Bakken L., Jiang Q.Q., Nes I.F. Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Syst. Appl. Microbiol. 18:1995;549-559.
50. Voytek M.A., Ward B.B. Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl. Environ. Microbiol. 61:1995;1444-1450.
51. Ward B.B. Nitrification in marine environments. Nitrification Spec. Publ. Soc. Gen. Microbiol. vol. 20:1986;157-184 IRL Press, Oxford.
52. Ward B.B., Zafiriou O.C. Nitrification and nitric oxide in the oxygen minimum of the eastern tropical North Pacific. Deep-Sea Res. 35:1988;1127-1142.
53. Wood P.M. Nitrification as a bacterial energy source. Nitrification Spec. Publ. Soc. Gen. Microbiol. vol. 20:1986;39-62 IRL Press, Oxford.
54. Zahn J.A., Dispirito A.A. Membrane-associated methane monooxygenase from Methylococcus capsulatus Bath. J. Bacteriol. 178:1996;1018-1029.