Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria

Applied and Environmental Microbiology

Volumn 74, Issue 14, 2008, Pages 4567-4573

  Quéméneur, Marianne ^a   Heinrich Salmeron, Audrey ^b   Muller, Daniel ^b,c   Lièvremont, Didier ^b   Jauzein, Michel ^d   Bertin, Philippe N ^b   Garrido, Francis ^a   Joulian, Catherine ^a  

^a BRGM   (France)

^b Université de Strasbourg   (France)

^c UNIVERSITÉ DE LYON   (France)

^d Faculté des Sciences et Technologies   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; RNA; SOIL POLLUTION; SURVEYS;

16S RRNA PHYLOGENY; ARSENITE-OXIDIZING BACTERIA; CATALYTIC SUBUNITS; COMPARATIVE ANALYSIS; ENVIRONMENTAL SURVEYS; ESSENTIAL AMINO ACIDS; EVOLUTIONARY RELATIONSHIPS; GAMMAPROTEOBACTERIA;

AEROBIC BACTERIA;

AMINO ACID; ARSENIC TRIOXIDE; BACTERIAL RNA; RNA 16S;

AMINO ACID; ARSENITE; BACTERIUM; COMPARATIVE STUDY; EVOLUTION; OXIDATION; PHYLOGENY; PROTEIN; RNA; SPECIES DIVERSITY; TAXONOMY;

AEROBIC BACTERIUM; ALPHAPROTEOBACTERIA; AMINO ACID SEQUENCE; AOXB GENE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BETAPROTEOBACTERIA; EVOLUTION; GAMMAPROTEOBACTERIA; HEALTH SURVEY; MESOPHILIC BACTERIUM; MICROBIAL DIVERSITY; NUCLEOTIDE SEQUENCE; OXIDATION; PHYLOGENY; PROTEIN MOTIF; SOIL POLLUTION; TAXONOMY;

ALPHAPROTEOBACTERIA; BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

EID: 47749137465     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02851-07     Document Type: Article

References (44)

1. Anderson, G. L., J. Williams, and R. Hille. 1992. The purification and characterization of arsenite oxidase from Alcaligenes faecalis, a molybdenum-containing hydroxylase. J. Biol. Chem. 267:23674-23682.
2. Battaglia-Brunet, F., M.-C. Dictor, F. Garrido, C. Crouzet, D. Morin, K. Dekeyser, M. Clarens, and P. Baranger. 2002. An arsenic(III)-oxidizing bacterial population: selection, characterization, and performance in reactors. J. Appl. Microbiol. 93:656-667.
3. Battaglia-Brunet, F., C. Joulian, F. Garrido, M.-C. Dictor, D. Morin, K. Coupland, D. Barrie Johnson, K. B. Hallberg, and P. Baranger. 2006. Oxidation of arsenite by Thiomonas strains and characterization of Thiomonas arsenivorans sp. nov. Antonie van Leeuwenhoek 89:99-108.
4. Battaglia-Brunet, F., Y. Itard, F. Garrido, F. Delorme, C. Crouzet, C. Greffié, and C. Joulian. 2006. A simple biogeochemical process removing arsenic from a mine drainage water. Geomicrobiol. J. 23:1-11.
5. Braker, G., J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities. Appl. Environ. Microbiol. 66:2096-2104.
6. Case, R. J., Y. Boucher, I. Dahllöf, C. Holmström, W. F. Doolittle, and S. Kjelleberg. 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol. 73:278-288.
7. Coupland, K., F. Battaglia-Brunet, K. B. Hallberg, M.-C. Dictor, F. Garrido, and D. B. Johnson. 2004. Oxidation of iron, sulfur and arsenic in mine waters and mine wastes: an important role for novel Thiomonas spp., p. 639-646. In M. Tsezos, A. Hatzikioseyian, and E. Remoudaki (ed.), Biohydrometallurgy: a sustainable technology in evolution. National Technical University of Athens, Zografou, Greece.
8. Donahoe-Christiansen, J., S. D'Imperio, C. R. Jackson, W. P. Inskeep, and T. R. McDermott. 2004. Arsenite-oxidizing Hydrogenobaculum strain isolated from an acid-sulfate-chloride geothermal spring in Yellowstone National Park. Appl. Environ. Microbiol. 70:1865-1868.
9. Ellis, P. J., T. Conrads, R. Hille, and P. Kuhn. 2001. Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å. Structure 9:125-132.
10. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
12. Friedrich, M. W. 2002. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphosulfate reductase genes among sulfate-reducing microorganisms. J. Bacteriol. 184:278-289.
13. Gihring, T. M., G. K. Druschel, R. B. McCleskey, R. J. Hamers, and J. F. Banfield. 2001. Rapid arsenite oxidation by Thermus aquaticus and Thermus thermophilus: field and laboratory investigations. Environ. Sci. Technol. 35:3857-3862.
14. Green, H. H. 1918. Isolation and description of a bacterium causing oxidation of arsenite to arsenate in cattle-dipping baths. Rep. Dir. Vet. S. Afr. 6:593-599.
15. Hallberg, K. B., and D. B. Johnson. 2003. Novel acidophiles isolated from moderately acidic mine drainage waters. Hydrometallurgy 71:139-148.
16. Inskeep, W. P., R. E. Macur, N. Hamamura, T. P. Warelow, S. A. Ward, and J. M. Santini. 2007. Detection, diversity and expression of aerobic bacterial arsenite oxidase genes. Environ. Microbiol. 9:934-943.
17. Jackson, C. R., H. W. Langner, J. Donahoe-Christiansen, W. P. Inskeep, and T. R. McDermott. 2001. Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring. Environ. Microbiol. 3:532-542.
18. Jackson, C. R., and S. L. Dugas. 2003. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol. Biol. 23:3-18.
19. Joubert, A. V. P., L. Lucas, F. Garrido, C. Joulian, and M. Jauzein. 2007. Effect of temperature, gas phase composition, pH and microbial activity on As, Zn, Pb and Cd mobility in selected soils in the Ebro and Meuse Basins in the context of global change. Environ. Pollut. 148:749-758.
20. 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, NY.
21. Kashyap, D. R., L. M. Botero, W. L. Franck, D. J. Hassett, and T. R. McDermott. 2006. Complex regulation of arsenite oxidation in Agrobacterium iumefaciens. J. Bacteriol. 188:1081-1088.
22. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J. Mol. Biol. 16:111-120.
23. Klein, M., M. Friedrich, A. J. Roger, P. Hugenholtz, S. Fishbain, H. Abicht, L. L. Blackall, D. A. Stahl, and M. Wagner. 2001. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol. 183:6028-6035.
24. Lebrun, E., M. Brugna, F. Baymann, D. Muller, D. Lièvremont, M.-C. Lett, and W. Nitschke. 2003. Arsenite oxidase, an ancient bioenergetic enzyme. Mol. Biol. Evol. 20:686-693.
25. Mokashi, S. A., and K. M. Paknikar. 2002. Arsenic (III) oxidizing Microbacterium lacticum and its use in the treatment of arsenic contaminated groundwater. Lett. Appl. Microbiol. 34:258-262.
26. Muller, D., D. Lièvremont, D. D. Simeonova, J.-C. Hubert, and M.-C. Lett. 2003. Arsenite oxidase aox genes from a metal-resistant β-proteobacterium. J. Bacteriol. 185:135-141.
27. Muller, D., C. Médigue, S. Koechler, V. Barbe, M. Barakat, E. Talla, V. Bonnefoy, E. Krin, F. Arsène-Ploetze, C. Carapito, M. Chandler, B. Cournoyer, S. Cruveiller, C. Dossat, S. Duval, M. Heymann, E. Leize, A. Lieutaud, D. Lièvremont, Y. Makita, S. Mangenot, W. Nitschke, P. Ortet, N. Perdrial, B. Schoepp, P. Siguier, D. D. Simeonova, Z. Rouy, B. Segurens, E. Turlin, D. Vallenet, A. Van Dorsselaer, S. Weiss, J. Weissenbach, M.-C. Lett, A. Danchin, and P. N. Bertin. 2007. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet. 3:e53.
28. Petri, R., L. Podgorsek, and J. F. Imhoff. 2001. Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. FEMS Microbiol. Lett. 197:171-178.
29. Phillips, S. E., and M. L. Taylor. 1976. Oxidation of arsenite to arsenate by Alcaligenes faecalis. Appl. Environ. Microbiol. 32:392-399.
30. Pierson, B. K., and R. W. Castenholz. 1974. A phototrophic gliding filamentous bacterium of hot springs, Chloroflexus aurantiacus, gen. and sp. nov. Arch. Microbiol. 100:5-24.
31. Rhine, E. D., S. M. Ni Chadhain, G. J. Zylstra, and L. Y. Young. 2007. The arsenite oxidase genes (aroAB) in novel chemoautotrophic arsenite oxidizers. Biochem. Biophys. Res. Commun. 354:662-667.
32. Rose, T. M., E. R. Schultz, J. G. Henikoff, S. Pietrokovski, C. M. McCallum, and S. Henikoff. 1998. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26:1628-1635.
33. Rozas, J., J. C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
34. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
35. Salmassi, T. M., J. J. Walker, D. K. Newman, J. R. Leadbetter, N. R. Pace, and J. G. Hering. 2006. Community and cultivation analysis of arsenite oxidizing biofilms at Hot Creek. Environ. Microbiol. 8:50-59.
36. Santini, J. M., and R. N. vanden Hoven. 2004. Molybdenum- containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26. J. Bacteriol. 186:1614-1619.
37. Scala, D. J., and L. J. Kerkhof. 1999. Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 65:1681-1687.
38. Silver, S., and L. T. Phung. 2005. Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol. 71:599-608.
39. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
40. vanden Hoven, R. N., and J. M. Santini. 2004. Arsenite oxidation by the heterotroph Hydrogenophaga sp. str. NT-14: the arsenite oxidase and its physiological electron acceptor. Biochim. Biophys. Acta 1656:148-155.
41. Van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10:569-570.
42. Wagner, M., A. J. Roger, J. L. Flax, G. A. Brusseau, and D. A. Stahl. 1998. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol. 180:2975-2982.
43. Weeger, W., D. Lièvremont, M. Perret, F. Lagarde, J.-C. Hubert, M. Leroy, and M.-C. Lett. 1999. Oxidation of arsenite to arsenate by a bacterium isolated from an aquatic environment. Biometals 12:141-149.
44. Xia, X., and Z. Xie. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92:371-373.