Impacts of Organic and Inorganic Fertilizers on Nitrification in a Cold Climate Soil are Linked to the Bacterial Ammonia Oxidizer Community

Microbial Ecology

Volumn 62, Issue 4, 2011, Pages 982-990

  Fan, Fenliang ^a   Yang, Qianbao ^a   Li, Zhaojun ^a   Wei, Dan ^b   Cui, Xi'an ^b   Liang, Yongchao ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b HEILONGJIANG ACADEMY OF AGRICULTURAL SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; AMMONIA MONOOXYGENASE; ARCHAEAL DNA; BACTERIAL DNA; FERTILIZER; OXIDOREDUCTASE;

ARCHAEAL GENE; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIUM; CHINA; COLD CLIMATE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; NITRIFICATION; SOIL;

AMMONIA; ARCHAEA; BACTERIA; CHINA; COLD CLIMATE; DNA, ARCHAEAL; DNA, BACTERIAL; FERTILIZERS; GENES, ARCHAEAL; GENES, BACTERIAL; NITRIFICATION; OXIDOREDUCTASES; SOIL; SOIL MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 80255132762     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-9897-5     Document Type: Article

References (43)

1. Avrahami S, Bohannan BJM (2007) Response of Nitrosospira sp. strain AF-like ammonia oxidizers to changes in temperature, soil moisture content, and fertilizer concentration. Appl Environ Microbiol 73: 1166-1173.
2. Avrahami S, Conrad R (2003) Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol 69: 6152-6164.
3. Avrahami S, Conrad R (2005) Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil? Can J Microbiol 51: 709-714.
4. Avrahami S, Liesack W, Conrad R (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ Microbiol 5: 691-705.
5. De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol and Biochem 33: 853-866.
6. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2: 621-624.
7. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ (2010) Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72: 386-394.
8. Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenström J, Hallin S (2007) Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biol and Biochem 39: 106-115.
9. Fan F, Zhang F, Lu Y (2011) Linking plant identity and interspecific competition to soil nitrogen cycling through ammonia oxidizer communities. Soil Biol and Biochem 43: 46-54.
10. Fierer N, Carney KM, Horner-Devine MC, Megonigal JP (2009) The biogeography of ammonia-oxidizing bacterial communities in soil. Microb Ecol 58: 435-445.
11. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688.
12. Francis CA, Beman JM, Kuypers MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 19-27.
13. Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74: 566-574.
14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, pp 95-98.
15. 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.
16. He J, Shen J, Zhang L, Zhu Y, Zheng Y, Xu M, Di H (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: 2364-2374.
17. Jia Z, Conrad R (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
18. Könneke M, Bernhard AE, De la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
19. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55: 485-529.
20. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
21. Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10: 2966-2978.
22. Oved T, Shaviv A, Goldrath T, Mandelbaum RT, Minz D (2001) Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 67: 3426-3433. doi: 10. 1128/aem. 67. 8. 3426-3433. 2001.
23. Pratscher J, Dumont MG, Conrad R (2011) Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil. Proc Natl Acad Sci USA 108: 4170-4175. doi: 10. 1073/pnas. 1010981108.
24. Prosser JI (1989) Autotrophic nitrification in bacteria. Adv Microb Physiol 30: 125-181.
25. Purkhold U, Pommerening-Roser A, Juretschko S, Schmid MC, Koops HP, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66: 5368-5382.
26. Richard CH, Maria Teresa C, Nerino M, Jon RS, Marco B, Alan JM (1997) Direct molecular biological analysis of ammonia oxidising bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol Ecol 23: 45-54.
27. 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.
28. Schauss K, Focks A, Leininger S, Kotzerke A, Heuer H, Thiele-Bruhn S, Sharma S, Wilke BM, Matthies M, Smalla K (2009) Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ Microbiol 11: 446-456.
29. Schleper C (2010) Ammonia oxidation: different niches for bacteria and archaea? ISME J 4: 1092-1094.
30. Shen J, Zhang L, Zhu Y, Zhang J, He J (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 1601-1611.
31. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
32. Tan KH (2005) Soil sampling, preparation, and analysis. CRC Press, Boca Raton.
33. 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. doi: 10. 1128/AEM. 01324-10184.
34. Ter Braak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user's guide: software for canonical community ordination (version 4. 5). Microcomputer Power, Ithaca, NY: 1-500.
35. 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.
36. Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C (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.
37. Utaker JB, Bakken L, Jiang QQ, Nes IF (1996) Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Syst Appl Microbiol 18: 549-559.
38. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
39. 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.
40. Webster G, Embley TM, Prosser JI (2002) Grassland management regimens reduce small-scale heterogeneity and species diversity of {beta}-proteobacterial ammonia oxidizer populations. Appl Environ Microbiol 68: 20-30.
41. Wessén 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.
42. Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103: 12317-12322.
43. 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.