Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments

Applied and Environmental Microbiology

Volumn 72, Issue 10, 2006, Pages 6829-6832

  Penton, C Ryan ^a   Devol, Allan H ^b   Tiedje, James M ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIUM COMPOUNDS; ECOLOGY; MARINE BIOLOGY; OXIDATION; SEDIMENTS; SOILS;

ANAEROBIC AMMONIUM; ANAMMOX BACTERIA; MARINE SEDIMENTS;

BACTERIA;

AMMONIA; FRESH WATER; PRIMER DNA; RNA 16S;

AMMONIUM; ANOXIC SEDIMENT; BACTERIUM; FRESHWATER SEDIMENT; MARINE SEDIMENT; PERMAFROST; POPULATION DISTRIBUTION; SOIL;

AMMONIUM OXIDIZING BACTERIUM; ANAEROBIC BACTERIUM; ARTICLE; BACTERIUM; BACTERIUM DETECTION; BIOGEOCHEMISTRY; BROCADIA; ECOLOGY; GENE SEQUENCE; GEOGRAPHICAL VARIATION (SPECIES); KUENENIA; MARINE ENVIRONMENT; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; SCALINDUA; SEDIMENT; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SOIL; SOIL MICROFLORA; SPECIES DISTRIBUTION; SPECIES IDENTIFICATION;

BACTERIA, ANAEROBIC; FRESH WATER; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; QUATERNARY AMMONIUM COMPOUNDS; RNA, RIBOSOMAL, 16S; SEAWATER; WATER MICROBIOLOGY;

CANDIDATUS SCALINDUA; KUENENIA;

EID: 33750042897     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01254-06     Document Type: Article

References (24)

1. Bowman, J. P., and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl. Environ. Microbiol. 69:2463-2483.
2. Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33(Database Issue):D294-D296.
3. 2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422:606-608.
4. Dalsgaard, T., and B. Thamdrup. 2002. Factors controlling anaerobic ammonium oxidation with nitrite in marine sediments. Appl. Environ. Microiol. 68:3802-3808.
5. Devol, A. H. 2003. Nitrogen cycle-solution to a marine mystery. Nature 422:575-576.
6. Egli, K., U. Franger, P. J. J. Alvarez, H. R. Siegrist, J. R. Van der Meer, and A. J. B. Zehnder. 2001. Enrichment and characterization of an anammox bacterium from a rotating biological contractor treating ammonium-rich leachate. Arch. Microbiol. 175:198-207.
7. Freitag, T. E., and J. I. Prosser. 2003. Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl. Environ. Microbiol. 69:1359-1371.
8. Kirkpatrick, J., B. Oakley, C. Fuchsman, S. Srinivasan, J. T. Staley, and J. W. Murray. 2006. Diversity and distribution of planctomycetes and related bacteria in the suboxic zone of the Black Sea. Appl. Environ. Microbiol. 72:3079-3083.
9. Kuai, L., and W. Verstraete. 1998. Ammonium removal by the oxygen-limited autotrophic nitrification-denitrification system. Appl. Environ. Microbiol. 64:450-4506.
10. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5:150-163.
11. Kuypers, M. M. M., G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. B. Jørgensen, and M. S. M. Jetten. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 102:6478-6483.
12. Kuypers, M. M. M., A. O. Sliekers, G. Lavik, M. Schmid, B. B. Jørgensen, J. G. Kuenen, J. S. Sinninghe Damsté, M. Strous, and M. S. M. Jetten. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608-611.
13. Neef, A., R. I. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: in situ detection of Planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266.
14. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
15. Risgaard-Peterson, N., R. L. Meyer, M. Schmid, M. S. M. Jetten, A. Enrich-Prast, S. Rysgaard, and N. P. Revsbech. 2004. Anaerobic ammonium oxidation in an estuarine sediment. Aquat. Microb. Ecol. 36:293-304.
16. Schalk, J., H. Oustad, J. G. Kuenen, and M. S. M. Jetten. 1998. The anaerobic oxidation of hydrazine: a novel reaction in microbial nitrogen metabolism. FEMS Microbiol. Lett. 158:61-67.
17. Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, M. S. M. Jetten, J. Metzger, K.-H. Schleifer, and M. Wagner. 2000. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst. Appl. Microbiol. 23:93-106.
18. Schmid, M., K. Walsh, R. Webb, W. I. C. Rijpstra, K. T. van de Pas-Schoonen, M. J. Verbruggen, T. Hill, B. Moffett, J. Fuerst, S. Schouten, J. S. Sinninghe Damsté, J. Harris, P. Shaw, M. S. M. Jetten, and M. Strous. 2003. Candidatus "Scalindua brodae," sp. nov., Candidates "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria. Syst. Appl. Microbiol. 26:529-538.
19. Schmid, M. C., B. Maas, A. Dapena, K. van de Pas-Schoonen, J. van de Vossenberg, B. Kartal, L. van Niftrik, I. Schmidt, I. Cirpus, J. G. Kuenen, M. Wagner, J. S. Sinninghe Damsté, M. Kuypers, N. P. Revsbech, R. Mendez, M. S. M. Jetten, and M. Strous. 2005. Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria. Appl. Environ. Microbiol. 71:1677-1684.
20. Strous, M., J. G. Kuenen, and M. S. M. Jetten. 1999. Key physiology of anaerobic ammonium oxidation. Appl. Environ. Microbiol. 65:3248-3250.
21. Tal, Y., J. E. M. Watts, and H. J. Schreier. 2005. Anaerobic ammonia-oxidizing bacteria and related activity in Baltimore inner harbor sediment. Appl. Environ. Microbiol. 71:1816-1821.
22. Trimmer, M., J. C. Nicholls, and B. Deflandre. 2003. Anaerobic ammonium oxidation measured in sediments along the Thames estuary, United Kingdom. Appl. Environ. Microbiol. 69:6447-6454.
23. Van de Graaf, A., A. Mulder, P. de Bruijn, M. S. M. Jetten, L. Robertson, and J. Kuenen. 1995. Anaerobic oxidation of ammonium is a biologically mediated process. Appl. Environ. Microbiol. 61:1246-1251.
24. Vishnivetskaya, T., S. Kathariou, J. McGrath, D. Gilichinsky, and J. M. Tiedje. 2000. Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 4:165-173.