Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

ISME Journal

Volumn 6, Issue 11, 2012, Pages 2024-2032

  Taylor, Anne E ^a   Zeglin, Lydia H ^a   Wanzek, Thomas A ^a   Myrold, David D ^a   Bottomley, Peter J ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

ammonia; archaea; bacteria; nitrification; soil

Indexed keywords

AMMONIA; FERTILIZER;

AMMONIA; BACTERIUM; COMMUNITY COMPOSITION; COMPLEXITY; FALLOW; INHIBITOR; MICROBIAL ACTIVITY; MICROBIAL ECOLOGY; PERSISTENCE; POPULATION DYNAMICS; PROKARYOTE; RELATIVE ABUNDANCE; SOIL MICROORGANISM; WHEAT;

ARCHAEON; ARTICLE; BACTERIUM; CHEMISTRY; METABOLISM; MICROBIOLOGY; NITRIFICATION; OXIDATION REDUCTION REACTION; SOIL;

AMMONIA; ARCHAEA; BACTERIA; FERTILIZERS; NITRIFICATION; OXIDATION-REDUCTION; SOIL; SOIL MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 84867748286     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.51     Document Type: Article

References (32)

1. Adair KL, Schwartz E. (2008). Evidence that ammoniaoxidizing archaea are more abundant than ammoniaoxidizing bacteria in semiarid soils of northern Arizona, USA. Microbial Ecol 56: 420-426.
2. Berube PM, Samudrala R, Stahl DA. (2007). Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol 189: 3935-3944.
3. Bollmann A, Schmidt I, Saunders AM, Nicolaisen MH. (2005). Influence of starvation on potential ammoniaoxidizing activity and amoA mRNA levels of Nitrosospira briensis. Appl Environ Microbiol 71: 1276-1282.
4. Boyle-Yarwood SA, Bottomley PJ, Myrold DD. (2008). Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environ Microbiol 10: 2956-2965.
5. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S et al. (2010). Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72: 386-394.
6. Hallin S, Jones CM, Schloter M, Philippot L. (2009). Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3: 597-605.
7. He J-Z, Shen J-P, Zhang L-M, Zhu Y-G, Zheng Y-M, Xu M-G et al. (2007). Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9: 3152-3152.
8. Horz HP, Rotthauwe JH, Lukow T, Liesack W. (2000). Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J Microbiol Methods 39: 197-204.
9. Jia ZJ, Conrad R. (2009). Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
10. Johnstone BH, Jones RD. (1988a). Physiological effects of long-term energy-source deprivation on the survival of a marine chemolithotrophic ammonium-oxidizing bacterium. Marine Ecol-Progress Series 49: 295-303.
11. Johnstone BH, Jones RD. (1988b). Recovery of a marine chemolithotrophic ammonium-oxidizing bacterium from long-term energy-source deprivation. Canadian J Microbiol 34: 1347-1350.
12. Jones RD, Morita RY, Koops HP, Watson SW. (1988). A new marine ammonium-oxidizing bacterium, Nitrosomonas Cryotolerans Sp-Nov. Canadian J Microbiol 34: 1122-1128.
13. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
14. McCune B, Mefford MJ. (1999). PC-ORD. Multivariate Analysis of Ecological Data. Version 4. MjM Software, Gleneden Beach, Oregon, USA.
15. Mertens J, Broos K,Wakelin SA, Kowalchuk GA, Springael D, Smolders E. (2009). Bacteria, not archaea, restore nitrification in a zinc-contaminated soil. ISME J 3: 916-923.
16. Mintie AT, Heichen RS, Cromack K, Myrold DD, Bottomley PJ. (2003). Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon cascade mountains. Appl Environ Microbiol 69: 3129-3136.
17. Norton JM. (2008). Nitrification in agricultural soils. In: Schepers JS, Raun WR (eds). Nitrogen in Agricultural Systems. American Society of Agronomy, Inc., Crop Science Society of America, Inc., Soil Science Society of America, Inc.: Madison, WI, pp 173-200.
18. Offre P, Prosser JI, Nicol GW. (2009). Growth of ammoniaoxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiol Ecol 70: 99-108.
19. Peterson RG, Calvin LD. (1996). Sampling. In Methods of Soil Analysis, Part 3-Chemical Methods. Sparks DL (ed). Soil Science Society of Ameria: Madison, Wisconsin, pp 1-18.
20. Rotthauwe JH,Witzel KP, Liesack W. (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.
21. Schauss K, Focks A, Leininger S, Kotzerke A, Heuer H, Thiele-Bruhn S et al. (2009). Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ Microbiol 11: 446-456.
22. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ. (2008). Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 1601-1611.
23. Shi W, Miller BE, Stark JM, Norton JM. (2004). Microbial nitrogen transformations in response to treated dairy waste in agricultural soils. Soil Sci Soc America J 68: 1867-1874.
24. Taylor AE, Zeglin LH, Dooley S, Myrold DD, Bottomley PJ. (2010). Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils. Appl Environ Microbiol 76: 7691-7698.
25. Tourna M, Freitag TE, Nicol GW, Prosser JI. (2008). Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10: 1357-1364.
26. Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T et al. (2011). Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 108: 8420-8425.
27. Verhamme DT, Prosser JI, Nicol GW. (2011). Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5: 1067-1071.
28. Wessen E, Nyberg K, Jansson JK, Hallin S. (2010). Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management. Appl Soil Ecol 45: 193-200.
29. Wessen E, Soderstrom M, Stenberg M, Bru D, Hellman M, Welsh A et al. (2011). Spatial distribution of ammoniaoxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning. ISME J 5: 1213-1225.
30. Xia W, Zhang C, Zeng X, Feng Y, Weng J, Lin X et al. (2011). Autotrophic growth of nitrifying community in an agricultural soil. ISME J 5: 1226-1236.
31. Zeglin L, Taylor AE, Bottomley PJ, Myrold DD. (2011). Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses. Environ Microbiol Reports 3: 717-726.
32. Zhang LM, Offre PR, He JZ, Verhamme DT, Nicol GW, Prosser JI. (2010). Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci USA 107: 17240-17245.