Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues

Applied and Environmental Microbiology

Volumn 76, Issue 7, 2010, Pages 2155-2164

  Henderson, Sherri L ^a,b   Dandie, Catherine E ^a,e   Patten, Cheryl L ^b   Zebarth, Bernie J ^a   Burton, David L ^c   Trevors, Jack T ^d   Goyer, Claudia ^a  

^a FREDERICTON RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b UNIVERSITY OF NEW BRUNSWICK   (Canada)

^c DALHOUSIE UNIVERSITY   (Canada)

^d UNIVERSITY OF GUELPH   (Canada)

^e CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMENDED SOIL; C:N RATIO; CROP RESIDUE; CROPPING SYSTEMS; DENITRIFICATION RATE; DENITRIFIERS; DRY SOIL; IN-PLANTS; INCUBATION PERIODS; MRNA LEVEL; NITROUS OXIDE; NITROUS OXIDE EMISSIONS; PLANT RESIDUES; RED CLOVER; SOIL MICROCOSMS; TREATED SOILS;

AGRICULTURAL WASTES; ANESTHETICS; DENITRIFICATION; GLUCOSE; NITROGEN OXIDES; ORGANIC CARBON;

SOILS;

CARBON; GLUCOSE; MESSENGER RNA; NITRATE; NITRITE; NITROGEN; NITROUS OXIDE;

ABUNDANCE; CROP RESIDUE; DENITRIFICATION; GENE EXPRESSION; MICROBIAL COMMUNITY; MICROCOSM; NITROUS OXIDE; ORGANIC CARBON; SOIL AMENDMENT; SOIL MICROORGANISM;

ANAEROBIC GROWTH; ARTICLE; BARLEY; CLOVER; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PLANT; SOYBEAN;

ANAEROBIOSIS; CARBON; GENE EXPRESSION PROFILING; GLUCOSE; HORDEUM; METAGENOME; MOLECULAR SEQUENCE DATA; NITRATES; NITRITES; NITROGEN; NITROUS OXIDE; OXIDATION-REDUCTION; PLANTS; RNA, MESSENGER; SOIL MICROBIOLOGY; SOYBEANS; TRIFOLIUM;

GLYCINE MAX; HORDEUM; PSEUDOMONAS; PSEUDOMONAS MANDELII; TRIFOLIUM PRATENSE;

EID: 77950289122     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02993-09     Document Type: Article

References (40)

1. Araki, N., Y. Tsukamoto, A. Nagano, T. Yamaguchi, and H. Harada. 2006. Real time PCR quantification of nitrite reductase (nirS) genes in nitrogen removing fluidized bed reactor. Water Sci. Technol. 53:59-65.
2. Aulakh, M. S., J. W. Doran, D. T. Walters, A. R. Mosier, and D. D. Francis. 1991. Crop residue type and placement effects on denitriflcation and mineralization. Soil Sci. Soc. Am. J. 55:1020-1025.
3. Baggs, E. M., R. M. Rees, K. A. Smiths, and A. J. A. Vinter. 2000. Nitrous oxide emissions from soils after incorporating crop residues. Soil Use Manage. 16:82-87.
4. 2O emissions from soils at different water-filled pore space. Biol. Fertil. Soils 41:379-388.
5. Beauchamp, E. G., J. T. Trevors, and R. W. Paul. 1989. Carbon substrates for bacterial denitrification, p. 113-142. In B. A. Stewart (ed.), Advances in soil science, vol.10. Springer-Verlag Inc., New York, NY.
6. Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legier, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitriflcation conditions. J. Bacteriol. 188:7005-7015.
7. Betlach, M. R., and J. M. Tiedje. 1981. Kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification. Appl. Environ. Microbiol. 42:1074-1084.
8. Braker, G., J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje. 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.
9. Bremner, J. M. 1996. Nitrogen-total, p. 961-1010. In D. L. Sparks (ed.), Methods of soil analysis: chemical methods, part 3. Soil Science Society of America, Madison, WI.
10. 15N. Soil Biol. Biochem. 27:839-844.
11. Clays-Josserand, A., J. F. Ghiglion, L. Philippot, P. Lemanceau, and R. Lensi. 1999. Effect of soil types and plant species on the fluorescent pseudomonads nitrate dissimilating community. Plant Soil 209:275-282.
12. Dandie, C. E., D. L. Burton, B. J. Zebarth, J. T. Trevors, and C. Goyer. 2007. Analysis of denitrification genes and comparison of nosZ, cnorB, and 16S rDNA from culturable denitrifiying bacteria in potato cropping systems. Syst. Appl. Microbiol. 30:128-138.
13. Dandie, C. E., M. N. Miller, D. L. Burton, B. J. Zebarth, J. T. Trevors, and C. Goyer. 2007. Nitric oxide reductase-targeted real-time FCR quantification of denitrifler populations in soil. Appl. Environ. Microbiol. 73:4250-4358.
14. de Catanzaro, J. B., and E. G. Beauchamp. 1985. The effect of some carbon substances on denitrification rates and carbon utilization in soil. Biol. Fertil. Soils 1:183-187.
15. Delorme, S., P. Lemanceau, R. Christen, T. Corberand, J. M. Meyer, and L. Garden. 2002. Pseudomonas Hni sp. nov., a novel species from bulk and rhizospheric soils. Int. J. Syst. Evol. Microbiol. 52:513-523.
16. Dong, L. F., C. J. Smith, S. Papaspyrou, A. Stott, A. M. Osborn, and D. B. Nedwell. 2009. Changes in benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Appl. Environ. Microbiol. 75:3171-3179.
17. Drury, C. F., X. M. Yang, W. D. Reynolds, and C. S. Tan. 2004. Influences of crop rotation and aggregate size on carbon dioxide production in denitrification. Soil Tillage 79:87-100.
18. Gillam, K. M., B. J. Zebarth, and D. L. Burton. 2008. Nitrous oxide emissions from denitrification and the partitioning of gaseous losses as affected by nitrate and carbon addition and soil aeration. Can. J. Soil Sci. 88:133-143.
19. Greets, J., M. de Cooman, L. Wittebolle, K. Heylen, S. Vanparys, P. de Vos, W. Verstraete, and N. Boon. 2007. Real time PCR assays for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Appl. Microbiol. Biotechnol. 95:211-221.
20. Griffiths, R. I., A. S. Whiteley, A. G. O'Donnell, and M. J. Bailey. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRN A-based microbial community composition. Appl. Environ. Microbiol. 66:5488-5491.
21. Henry, S., E. Baudoin, J. C. Lopez-Gutierrez, F. Martin-Laurent, A. Brauman, and L. Philippot. 2004. Quantification of denitrifying bacteria in nirK gene targeted real time PCR. J. Microbiol. Methods 59:327-335.
22. Henry, S., D. Bru, B. Stres, S. Hallet, and L. Philippot. 2006. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl. Environ. Microbiol. 72:5181-5189.
23. Henry, S., S. Texier, S. Hallet, D. Bru, C. Dambreville, D. Cheneby, F. Bizouard, J. C. Germon, and L. Philippot. 2008. Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates. Environ. Microbiol. 10:3082-3092.
24. Huang, Y., J. Zou, X. Zheng, Y. Wang, and X. Xu. 2004. Nitrous oxide emissions as influenced by amendment of plant residues with different C:N ratios. Soil Biol. Biochem. 36:973-981.
25. Janzen, H. H., and R. M. N. Kucey. 2006. C, N. and S mineralization of crop residues as influences by crop species and nutrient regime. Plant Soil 106: 35-41.
26. Kandeler, E., K. Deiglmayr, D. Tscherko, D. Bru, and L. Philippot. 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.
27. 3 effects on the denitrification process. Plant Soil 138:273-286.
28. Kumar, K., and K. M. Goh. 2000. Crop residues and management practices: effects on soil quality, soil nitrogen dynamics, crop yield and nitrogen recovery. Adv. Agron. 68:167-319.
29. Lashof, D. A., and D. R. Ahuja. 1990. Relative contributions of greenhouse gas emissions to global warming. Nature 334:529-531.
30. 2O emissions and denitrifler community abundance in soil. Soil Biol. Biochem. 40:2553-11562
31. 2O emissions. Soil Sci. Soc. Am. J. 73:760-768.
32. Nelson, E. W., and L. E. Sommers. 1996. Total carbon, organic carbon, and organic matter, p. 1085-1122. In D. L. Sparks (ed.), Methods of soil analysis: chemical methods, part 3. Soil Science Society of America, Madison, WI.
33. Nijburg, J. W., M. J. L. Coolen, S. Gerads, P. J. A. K. Gunnewiek, and H. J. Laanbroek. 1997. Effects of nitrate availability and the presence of Glyceria maxima on the composition and activity of the dissimilatory nitrate-reducing bacterial community. Appl. Environ. Microbiol. 63:931-937.
34. Saleh-Lakha, S., K. E. Shannon, S. L. Henderson, B. J. Zebarth, D. L. Burton, C. Goyer, and J. T. Trevors. 2009. Effect of nitrate and acetylene on nirS, cnorB, and nosZ expression and denitrification activity in Pseudomonas mandelii. Appl. Environ. Microbiol. 75:5082-5087.
35. Sharma, S., Z. Szele, R. Schilling, J. C. Munch, and M. Schloter. 2006. Influence of freeze-thaw stress on the structure and function of microbial communities and denitrifying populations in soil. Appl. Environ. Microbiol. 72:2148-2154.
36. Smith, C. J., D. B. Nedwell, L. F. Dong, and A. M. Osborn. 2007. Diversity and abundance of nitrate reductase genes (narG and nap A), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl. Environ. Microbiol. 73:3612-3622.
37. Thorup-Kristensen, K., J. Magid, and J. S. Jensen. 2003. Catch crops and green manures as biological tools in nitrogen management in temperate zones. Adv. Agron. 79:227-302.
38. Throbäck, I. N., K. Enwall, A. Javis, and S. Hallin. 2004. Reassessing PCR primers targeting nirS, nirS, and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49:401-417.
39. Tiedje, J. M., A. J. Sexstone, D. D. Myrold, and J. A. Robinson. 1982. Denitrification: ecological niches, competition and survival. Antonie von Leeuwenhoek 48:569-583.
40. Verhille, S., N. Baida, F. Dabboussi, D. Izard, and H. Leclerc. 1999. Taxonomie study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov. Syst. Appl. Microbiol. 22:45-58.