Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities

Microbes and Environments

Volumn 27, Issue 4, 2012, Pages 519-524

  Yamamoto, Nozomi ^a   Oishi, Ryu ^a   Suyama, Yoshihisa ^a   Tada, Chika ^a   Nakai, Yutaka ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

Ammonia oxidizing archaea (AOA); Ammonia oxidizing bacteria (AOB); Animal manure compost; PCR DGGE; Real time PCR

Indexed keywords

AMMONIA; ARCHAEAL DNA; BACTERIAL DNA; RNA 16S;

ANIMAL; ARCHAEON; ARTICLE; BACTERIUM; CATTLE; CHICKEN; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; MANURE; METABOLISM; MICROBIOLOGY; NITRIFICATION; OXIDATION REDUCTION REACTION; SWINE;

AMMONIA; ANIMALS; ARCHAEA; BACTERIA; CATTLE; CHICKENS; DNA, ARCHAEAL; DNA, BACTERIAL; MANURE; NITRIFICATION; OXIDATION-REDUCTION; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SWINE;

ANIMALIA; BOS; NITROSOMONADALES; NITROSOMONAS; SUIDAE;

EID: 84871107667     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.ME12053     Document Type: Article

References (35)

1. Bernal, M.P., J.A. Alburquerque, and R. Moral. 2009. Composting of animal manures and chemical criteria for compost maturity assessment. A review. Bioresour. Technol. 100:5444-5453.
2. de la Torre, J.R., C.B. Walker, A.E. Ingalls, M. Könneke, and D.A. Stahl. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10:810-818.
3. Erguder, T.H., N. Boon, L. Wittebolle, M. Marzorati, and W. Verstraete. 2009. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol. Rev. 33:855-869.
4. Hatzenpichler, R., E.V. Lebedeva, E. Spieck, K. Stoecker, A. Richter, H. Daims, and M. Wagner. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. U.S.A. 105:2134-2139.
5. Hornek, R., A. Pommerening-Röser, H.P. Koops, A.H. Farnleitner, N. Kreuzinger, A. Kirschner, and R.L. Mach. 2006. Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta-ammonia oxidizers in the environment. J. Microbiol. Methods 66:147-155.
6. Innerebner, G., B. Knapp, T. Vasara, M. Romantschuk, and H. Insam. 2006. Traceability of ammonia-oxidizing bacteria in compost-treated soils. Soil Biol. Biochem. 38:1092-1100.
7. 2O in a compost reactor treating organic household waste. J. Appl. Microbiol. 106:1502-1511.
8. Könneke, M., A.E. Bernhard, J.R. de la Torre, C.B. Walker, J.B. Waterbury, and D.A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546.
9. Koops, H.P., U. Purkhold, A. Pommerening, G. Timmermann, and M. Wagner. 2006. The lithoautotrophic ammonia-oxidizing bacteria, p. 778-811. In M. Dworkin, D. Falkow, E. Rosenberg, K.H. Dchleifer, and E. Stackebgandt (ed.), Prokaryotes Third Edition, volume 5. Springer, New York.
10. Kowalchuk, G.A., Z.S. Naoumenko, P.J.L. Derikx, A. Felske, J.R. Stephen, and I.A. Arkhlpchenko. 1999. Molecular analysis of ammonia-oxidizing bacteria of the ß subdivision of the class proteobacteria in compost and composted materials. Appl. Environ. Microbiol. 65:396-403.
11. Kowalchuk, G.A., and J.R. Stephen. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55:485-529.
12. Lee, Y.H., S.K. Kim, Y.H. Kim, Y.S. Jeong, M.G. Yun, J.J. Cho, J.M. Kim, H.D. Yun, and H. Kim. 2010. Archaeal diversity during composting of pig manure and mushroom cultural waste based on 16S rRNA sequence. J. Korean Soc. Appl. Biol. Chem. 53:230-236.
13. Lebedeva, E.V., M. Alawi, C. Fiencke, B. Namsaraev, E. Bock, and E. Spieck. 2005. Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone. FEMS Microbiol. Ecol. 54:297-306.
14. Leininger, S., T. Urich, M. Schloter, L. Schwark, J. Qi, G. Nicol, J. Prosser, S. Schuster, and C. Schleper. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809.
15. Limpiyakorn, T., F. Kurisu, Y. Sakamoto, and O. Yagi. 2007. Effects of ammonium and nitrite on communities and populations of ammonia-oxidizing bacteria in laboratory-scale continuous-flow reactors. FEMS Microbiol. Ecol. 60:501-512.
16. Maeda, K., S. Toyoda, R. Shimojima, T. Osada, D. Hanajima, R. Morioka, and N. Yoshida. 2010. Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammoniaoxidizing bacteria. Appl. Environ. Microbiol. 76:1555-1562.
17. Martens-Habbena, W., P. Berube, H. Urakawa, J. de la Torre, and D. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979.
18. Martins, O., and O. Dews. 1992. Loss of nitrogenous compounds during composting of animal wastes. Bioresour. Technol. 42:103-111.
19. Nicol, G.W., S. Leininger, C. Schleper, and J.I. Prosser. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol. 10:2966-2978.
20. Oishi, R., C. Tada, R. Asano, N. Yamamoto, Y. Suyama, and Y. Nakai. 2012. Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations. Microb. Ecol. 63:787-793.
21. Park, H.D., G.F. Wells, H. Bae, C.S. Criddle, and C.A. Francis. 2006. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl. Environ. Microbiol. 72:5643-5647.
22. Reigstad, L.J., A. Richter, H. Daims, T. Urich, L. Schwark, and C. Schleper. 2008. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol. Ecol. 64:167-174.
23. Rotthauwe, J.H., K.P. Witzel KP, and W. Liesack. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-4712.
24. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
25. Tang, J.C., T. Kanamori, Y. Inoue, T. Yasuta, S. Yoshida, and A. Katayama. 2004. Changes in the microbial community structure during thermophilic composting of manure as detected by the quinone profile method. Process Biochem. 39:1999-2006.
26. Tourna, M., T.E. Freitag, G.W. Nicol, and J.I. Prosser. 2008. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 10:1357-1364.
27. Tourna, M., M. Stieglmeier, A. Spang, et al. 2011. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc. Natl. Acad. Sci. U.S.A. 108:8420-8425.
28. Treusch, A.H., S. Leininger, A. Kletzin, S.C. Schuster, H.P. Klenk, and C. Schleper. 2005. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 7:1985-1995.
29. Vuorinen, A.H., and M.H. Saharinen. 1997. Evolution of microbiological and chemical parameters during manure and straw cocomposting in a drum composting system. Agric. Ecosyst. Environ. 66:19-29.
30. Wells, G., H. Park, C. Yeung, B. Eggleston, C. Francis, and C. Criddle. 2009. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ. Microbiol. 11:2310-2328.
31. Yamamoto, N., R. Asano, H. Yoshii, K. Otawa, and Y. Nakai. 2011. Archaeal community dynamics and detection of ammoniaoxidizing archaea during composting of cattle manure using cultureindependent DNA analysis. Appl. Microbiol. Biotechnol. 90:1501-1510.
32. Yamamoto, N., K. Otawa, and Y. Nakai. 2010. Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting. Microb. Ecol. 60:807-815.
33. Zhang, C.L., Q. Ye, Z. Huang, et al. 2008. Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl. Environ. Microbiol. 74:6417-6426.
34. Zhang, T., T. Jin, Q. Yan, M. Shao, G. Wells, C. Criddle, and H.H.P. Fang. 2009. Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants. J. Appl. Microbiol. 107:970-977.
35. Zeng, G., J. Zhang, Y. Chen, et al. 2011. Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting. Bioresour. Technol. 102:9026-9032.