Impact of Long-Term Fertilization on the Composition of Denitrifier Communities Based on Nitrite Reductase Analyses in a Paddy Soil

Microbial Ecology

Volumn 60, Issue 4, 2010, Pages 850-861

  Chen, Zhe ^a,b   Luo, Xiqian ^a,c   Hu, Ronggui ^c   Wu, Minna ^a   Wu, Jinshui ^a   Wei, Wenxue ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; FERTILIZER; NITRITE REDUCTASE;

ARTICLE; BACTERIUM; CLASSIFICATION; ENZYMOLOGY; GENE DOSAGE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOIL;

BACTERIA; BACTERIAL PROTEINS; FERTILIZERS; GENE DOSAGE; MOLECULAR SEQUENCE DATA; NITRITE REDUCTASES; PHYLOGENY; SOIL; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 78149470564     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9700-z     Document Type: Article

References (43)

1. Henry S, Baudoin E, Lopez-Gutierrez JC, Martin-Laurent F, Baumann A, Philippot L (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J Microbiol Meth 59: 327-335.
2. Albritton DL, Meira Filho LG, Cubasch U (2001) Climate change 2001: the scientific basis. Contributions of Working Group I to the third assessment report of the Intergovernmental Panel on Climate Change. IPCC, Cambridge University Press.
3. Huang S, Pant HK, Lu J (2007) Effects of water regimes on nitrous oxide emission from soils. Ecol Eng 31: 9-15.
4. Hwang SJ, Hanaki K (2000) Effects of oxygen concentration and moisture content of refuse on nitrification, denitrification and nitrous oxide production. Bioresour Technol 71: 159-165.
5. Bergsma TT, Robertson GP, Ostrom NE (2002) Influence of soil moisture and land use history on denitrification end-products. J Environ Qual 31: 711-717.
6. 2O, and NO). Microbiol Rev 60: 609-640.
7. Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81: 1402-1414.
8. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143-169.
9. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-616.
10. Braker G, Zhou JZ, Wu LY, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities. Appl Environ Microbiol 66: 2096-2104.
11. Heylen K, Gevers D, Vanparys B, Wittebolle L, Geets J, Boon N, De Vos P (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8: 2012-2021.
12. 1 and nonheme copper nitrite reductase in denitrifying bacteria. Appl Environ Microbiol 55: 2924-2931.
13. Dambreville C, Hallet S, Nguyen C, Morvan T, Germon JC, Philippot L (2006) Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate. FEMS Microbiol Ecol 56: 119-131.
14. Enwall K, Philippot L, Hallin S (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71: 8335-8343.
15. Wolsing M, Prieme A (2004) Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiol Ecol 48: 261-271.
16. Tirol-Padre A, Tsuchiya K, Inubushi K, Ladha JK (2005) Enhancing soil quality through residue management in a rice-wheat system in Fukuoka, Japan. Soil Sci Plant Nutr 51: 849-860.
17. Surekha K, Kumari APP, Reddy MN, Satyanarayana K, Cruz PCS (2003) Crop residue management to sustain soil fertility and irrigated rice yields. Nutr Cycl Agroecosyst 67: 145-154.
18. FAO (2003) Selected indicators of food and agriculture development in Asia-Pacific region (1992-2002). RAP publication, pp 23-24.
19. 2. FEMS Microbiol Ecol 49: 445-454.
20. Cheneby D, Brauman A, Rabary B, Philippot L (2009) Differential responses of nitrate reducer community size, structure, and activity to tillage systems. Appl Environ Microbiol 75: 3180-3186.
21. Cai ZC, Xing GX, Yan XY, Xu H, Tsuruta H, Yagi K, Minami K (1997) Methane and nitrous oxide emissions from rice paddy fields as affected by nitrogen fertilizers and water management. Plant Soil 196: 7-14.
22. Yan X, Du L, Shi S, Xing G (2000) Nitrous oxide emission from wetland rice soil as affected by the application of controlled-availability fertilizers and mid-season aeration. Biol Fertil Soils 32: 60-66.
23. Porteous LA, Armstrong JL, Seidler RJ, Watrud LS (1994) An effective method to extract DNA from environmental samples for polymerase chain-reaction amplification and DNA fingerprint analysis. Curr Microbiol 29: 301-307.
24. Hallin S, Lindgren PE (1999) PCR detection of genes encoding nitrile reductase in denitrifying bacteria. Appl Environ Microbiol 65: 1652-1657.
25. Casciotti KL, Ward BB (2001) Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria. Appl Environ Microbiol 67: 2213-2221.
26. Throback IN, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49: 401-417.
27. Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-4376.
28. Bremer C, Braker G, Matthies D, Reuter A, Engels C, Conrad R (2007) Impact of plant functional group, plant species, and sampling time on the composition of nirK-type denitrifier communities in soil. Appl Environ Microbiol 73: 6876-6884.
29. Prieme A, Braker G, Tiedje JM (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68: 1893-1900.
30. Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64: 3769-3775.
31. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl Environ Microbiol 68: 5685-5692.
32. Alden L, Demoling F, Baath E (2001) Rapid method of determining factors limiting bacterial growth in soil. Appl Environ Microbiol 67: 1830-1838.
33. Katsuyama C, Kondo N, Suwa Y, Yamagishi T, Itoh M, Ohte N, Kimura H, Nagaosa K, Kato K (2008) Denitrification activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest. Microbes Environ 23: 337-345.
34. Yan TF, Fields MW, Wu LY, Zu YG, Tiedje JM, Zhou JZ (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol 5: 13-24.
35. Junier P, Kim OS, Witzel KP, Imhoff JF, Hadas O (2008) Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel. Aquat Microb Ecol 51: 129-140.
36. Falk S, Hannig M, Gliesche C, Wardenga R, Koster M, Jurgens K, Braker G (2007) nirS-containing denitrifier communities in the water column and sediment of the Baltic Sea. Biogeosciences 4: 255-268.
37. Jones CM, Hallin S (2010) Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME J 4: 633-641.
38. Smith JM, Ogram A (2008) Genetic and functional variation in denitrifier populations along a short-term restoration chronosequence. Appl Environ Microbiol 74: 5615-5620.
39. Cao YP, Green PG, Holden PA (2008) Microbial community composition and denitrifying enzyme activities in salt marsh sediments. Appl Environ Microbiol 74: 7585-7595.
40. Parkin TB (1987) Soil microsites as a source of denitrification variability. Soil Sci Soc Am J 51: 1194-1199.
41. Kandeler E, Deiglmayr K, Tscherko D, Bru D, Philippot L (2006) Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland. Appl Environ Microbiol 72: 5957-5962.
42. Jones CM, Stres B, Rosenquist M, Hallin S (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25: 1955-1966.
43. Yoshida M, Ishii S, Otsuka S, Senoo K (2009) Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biol Biochem 41: 2044-2051.