Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

Nature

Volumn 464, Issue 7288, 2010, Pages 543-548

  Ettwig, Katharina F ^a   Butler, Margaret K ^a,i   Le Paslier, Denis ^b,c,d   Pelletier, Eric ^b,c,d   Mangenot, Sophie ^b   Kuypers, Marcel M M ^e   Schreiber, Frank ^e   Dutilh, Bas E ^f   Zedelius, Johannes ^e   De Beer, Dirk ^e   Gloerich, Jolein ^g   Wessels, Hans J C T ^g   Van Alen, Theo ^a   Luesken, Francisca ^a   Wu, Ming L ^a   Van De Pas Schoonen, Katinka T ^a   Op Den Camp, Huub J M ^a   Janssen Megens, Eva M ^f   Francoijs, Kees Jan ^f   Stunnenberg, Henk ^f   Weissenbach, Jean ^b,c,d   Jetten, Mike S M ^a   Strous, Marc ^a,e,h   more..

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c Genoscope   (France)

^d UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^e MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^f RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^g RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^h BIELEFELD UNIVERSITY   (Germany)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROCARBON; METHANE; NITRITE; NITROUS OXIDE;

ANOXIC CONDITIONS; BACTERIUM; BIODEGRADATION; DETOXIFICATION; HYDROCARBON; METHANE; MICROBIAL ACTIVITY; NITRIC OXIDE; NITRITE; OXIDATION; PHOTOSYNTHESIS; RESPIRATION;

ANAEROBIC METABOLISM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; DENITRIFICATION; DENITRIFYING BACTERIUM; GENE EXPRESSION; METHYLOMIRABILIS OXYFERA; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ANAEROBIOSIS; BACTERIA; GENOME, BACTERIAL; METHANE; MOLECULAR SEQUENCE DATA; NITRITES; OXIDATION-REDUCTION; OXYGEN; OXYGENASES; PHYLOGENY; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 77950258771     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08883     Document Type: Article

References (51)

1. Galloway, J. N. et al. Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320, 889-892 (2008).
2. Bodelier, P. L. E. & Laanbroek, H. J. Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol. Ecol. 47, 265-277 (2004).
3. Raghoebarsing, A. A. et al. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440, 918-921 (2006).
4. Ettwig, K. F., van Alen, T., van de Pas-Schoonen, K. T., Jetten, M. S. M. & Strous, M. Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum. Appl. Environ. Microbiol. 75, 3656-3662 (2009).
5. Hu, S. et al. Enrichment of denitrifying anaerobic methane oxidizing microorganisms. Envir. Microbiol. Rep. 1, 377-384 (2009).
6. Rappé, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369-394 (2003).
7. Thauer, R. K. & Shima, S. Methane as fuel for anaerobic microorganisms. Ann. NY Acad. Sci. 1125, 158-170 (2008).
8. Trotsenko, Y. A. & Murrell, J. C. Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 63, 183-229 (2008).
9. Krüger, M. et al. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878-881 (2003).
10. Knittel, K. & Boetius, A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 63, 311-334 (2009).
11. Ettwig, K. F. et al. Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. Environ. Microbiol. 10, 3164-3173 (2008).
12. Wilmes, P., Simmons, S. L., Denef, V. J. & Banfield, J. F. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev. 33, 109-132 (2009).
13. Farrer, R. A., Kemen, E., Jones, J. D. G. & Studholme, D. J. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol. Lett. 291, 103-111 (2009).
14. Dutilh, B. E., Huynen, M. A. & Strous, M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics 25, 2878-2881 (2009).
15. Zumft, W. G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61, 533-616 (1997).
16. Heider, J. Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr. Opin. Chem. Biol. 11, 188-194 (2007).
17. Chistoserdova, L., Kalyuzhnaya, M. G. & Lidstrom, M. E. C1-transfer modules: from genomics to ecology. ASM News 71, 521-528 (2005).
18. Howard, C. S. & Daniels, F. Stability of nitric oxide over a long time interval. J. Phys. Chem. 62, 360-361 (1958).
19. Parvulescu, V. I., Grange, P. & Delmon, B. Catalytic removal of NO. Catal. Today 46, 233-316 (1998).
20. van Ginkel, C. G., Rikken, G. B., Kroon, A. G. M. & Kengen, S. W. M. Purification and characterization of chlorite dismutase: a novel oxygen-generating enzyme. Arch. Microbiol. 166, 321-326 (1996).
21. Bab-Dinitz, E., Shmuely, H., Maupin-Furlow, J., Eichler, J. & Shaanan, B. Haloferax volcanii PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families? Bioinformatics 22, 671-675 (2006).
22. Zumft, W. G. Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type. J. Inorg. Biochem. 99, 194-215 (2005).
23. Zumft, W. G. & Kroneck, P. M. H. in Advances in Microbial Physiology Vol. 52 (ed. Poole, R. K.) 107-227 (Academic, 2007).
24. Prior, S. D. & Dalton, H. Acetylene as a suicide substrate and active-site probe for methane monooxygenase from Methylococcus capsulatus (Bath). FEMS Microbiol. Lett. 29, 105-109 (1985).
25. 2O: a review. Rapid Commun. Mass Spectrom. 21, 3569-3578 (2007).
26. Demicheli, V., Quijano, C., Alvarez, B. & Radi, R. Inactivation and nitration of human superoxide dismutase (SOD) by fluxes of nitric oxide and superoxide. Free Radic. Biol. Med. 42, 1359-1368 (2007).
27. Allen, M. B. & van Niel, C. B. Experiments on bacterial denitrification. J. Bacteriol. 64, 397-412 (1952).
28. Broda, E. The history of inorganic nitrogen in the biosphere. J. Mol. Evol. 7, 87-100 (1975).
29. Fenchel, T. Origin and Early Evolution of Life (Oxford Univ. Press, 2002).
30. Castresana, J. in Respiration in Archaea and Bacteria: Diversity of Prokaryotic Electron Transport Carriers Vol. 15 (ed. Zannoni, D.) 1-14 (Springer, 2004).
31. Ducluzeau, A. L. et al. Was nitric oxide the first deep electron sink? Trends Biochem. Sci. 34, 9-15 (2009).
32. Chapman, D. J. & Schopf, J. W. Biological and Biochemical Effects of the Development of an Aerobic Environment (Princeton Univ. Press, 1983).
33. Holland, H. D. The oxygenation of the atmosphere and oceans. Phil. Trans. R. Soc. B 361, 903-915 (2006).
34. 4 in the atmosphere of early Earth. J. Geophys. Res. Planets 105, 11981-11990 (2000).
35. Hayes, J. M. in Earth's Earliest Biosphere (ed. Schopf, J. W.) 291-301 (Princeton Univ. Press, 1983).
36. Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316-322 (1996).
37. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
38. Vallenet, D. et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 34, 53-65 (2006).
39. Wilm, M. et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469 (1996).
40. Andersen, K., Kjær, T. & Revsbech, N. P. An oxygen insensitive microsensor for nitrous oxide. Sens. Actuators B Chem. 81, 42-48 (2001).
41. Revsbech, N. P. An oxygen microsensor with a guard cathode. Limnol. Oceanogr. 34, 474-478 (1989).
42. Schreiber, F., Polerecky, L. & de Beer, D. Nitric oxide microsensor for high spatial resolution measurements in biofilms and sediments. Anal. Chem. 80, 1152-1158 (2008).
43. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998).
44. Hakemian, A. S. & Rosenzweig, A. C. The biochemistry of methane oxidation. Annu. Rev. Biochem. 76, 223-241 (2007).
45. Stoecker, K. et al. Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc. Natl Acad. Sci. USA 103, 2363-2367 (2006).
46. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670 (2003).
47. Ishihama, Y., Rappsilber, J., Andersen, J. S. & Mann, M. Microcolumns with self-assembled particle frits for proteomics. J. Chromatogr. A 979, 233-239 (2002).
48. Weatherly, D. B. et al. A heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results. Mol. Cell. Proteomics 4, 762-772 (2005).
49. Raghoebarsing, A. A. New Directions in Microbial Methane Oxidation. PhD thesis, Radboud Univ. Nijmegen (2006).
50. Friedman, S. H., Massefski, W. & Hollocher, T. C. Catalysis of intermolecular oxygen atom transfer by nitrite dehydrogenase of Nitrobacter agilis. J. Biol. Chem. 261, 538-543 (1986).
51. McIlvin, M. R. & Altabet, M. A. Chemical conversion of nitrate and nitrite to nitrous oxide for nitrogen and oxygen isotopic analysis in freshwater and seawater. Anal. Chem. 77, 5589-5595 (2005).