Denitrifying bacteria in bulk and maize-rhizospheric soil: Diversity and N2O-reducing abilities

Canadian Journal of Microbiology

Volumn 50, Issue 7, 2004, Pages 469-474

  Cheneby D ^a   Perrez, S ^a   Devroe, C ^a   Hallet, S ^a   Couton, Y ^a   Bizouard, F ^a   Iuretig, G ^a   Germon, J C ^a   Philippot, L ^a  

^a CEMAGREF   (France)

Author keywords

Denitrification; Diversity; Maize; N2O; Rhizosphere

Indexed keywords

BACTERIA; CROPS; DNA; ECOSYSTEMS; NITRIFICATION;

DENITRIFYING BACTERIA; MAIZE PLANTED SOILS;

SOILS;

DNA 16S; NITRATE; NITROGEN; NITROUS OXIDE;

COMMUNITY STRUCTURE; DENITRIFICATION; MAIZE; MICROBIAL COMMUNITY; POLYMORPHISM; RHIZOSPHERE;

ARTICLE; BACTERIUM; BACTERIUM ISOLATION; COMMUNITY STRUCTURE; DENITRIFICATION; DENITRIFYING BACTERIUM; DNA RESTRICTION; ENRICHMENT CULTURE; GENE AMPLIFICATION; MAIZE; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REDUCTION; RHIZOBIUM; RHIZOSPHERE; SOIL;

BACTERIA; BIODIVERSITY; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; GENES, RRNA; MOLECULAR SEQUENCE DATA; NITRATES; NITRITES; NITROGEN; OXIDATION-REDUCTION; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOBIUM; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; ZEA MAYS;

AGROBACTERIUM; BACTERIA (MICROORGANISMS); NEGIBACTERIA; ZEA MAYS;

EID: 6344269193     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/w04-037     Document Type: Article

References (42)

1. Avrahami, S., and Conrad, R. 2003. Patterns of community change among ammonia oxidizers in meadows soils upon long-term incubation at different temperatures. Appl. Environ. Microbiol. 60: 6152-6164.
2. Berks, B.C., Ferguson, S.J., Moir, J.W.B., and Richardson, D.J.D. 1995. Enzymes and associated electron transports systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim. Biophys. Acta, 1232: 97-173.
3. Bothe, H., Jost, G., Schloter, M., Ward, B., and Witzel, K. 2000. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24: 673-690.
4. Braker, G., Fesefeldt, A., and Witzel, K.P. 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.
5. Braker, G., Zhou, J., Wu, L., Devol, A.H., and Tiedje, J.M. 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.
6. Cavigelli, M.A., and Robertson, G.P. 2001. Role of denitrifiers diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol. Biochem. 33: 297-310.
7. Chelius, M., and Triplett, E. 2001. The diversity of archea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 41: 252-263.
8. Chèneby, D., Philippot, L., Hartmann, A., Henault, C., and Germon, J.C. 2000. 16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils. FEMS Microbiol. Ecol. 34: 121-128.
9. Chèneby, D., Hallet, S., Mondon, M., Martin-Laurent, F., Germon, J.C., and Philippot, L. 2003. Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis. Microb. Ecol. 46: 113-121.
10. Clays-Josserand, A., Lemanceau, P., Philippot, L., and Lensi, R. 1995. Effect of soil type and plant species on the fluorescent pseudomonads nitrate dissimilating community. Plant Soil, 209: 275-282.
11. Gamble, T.N., Betlach, H.R., and Tiedje, J.M. 1977. Numerically dominant denitrifying bacteria from world soils. Appl. Environ. Microbiol. 33: 926-939.
12. Garcia, J. 1977. Analyse de différents groupes composant la microflore dénitrifiante de sols de rizière du Sénégal. Annals Microbiologie (Institut Pasteur), 128: 433-446.
13. Greenberg, E., and Becker, G. 1997. Nitrous oxide as end product of denitrification by strains of fluorescent pseudomonads. Can. J. Microbiol. 23: 903-907.
14. Hallin, S., and Lindgren, P.E. 1999. PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl. Environ. Microbiol. 65(4): 1652-1657.
15. Holtan-Hartwig, L., Dörsch, P., and Bakken, L.R. 2000. Comparison of denitrifying communities in organic soils: kinetics of NO3- and N2O reduction. Soil Biol. Biochem. 32: 833-843.
16. Kent, A., and Triplett, E.W. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu. Rev. Microbiol. 56: 211-236.
17. Kowalchuk, G., and Stephen, J. 2001. Ammonia-oxidizing bacteria: a model for molecular biology. Annu. Rev. Microbiol. 55: 485-529.
18. Kowalchuk, G.A., Stienstra, A.W., Heilig, G.H., Stephen, J.R., and Woldendorp, J.W. 2000. Molecular analysis of ammonia-oxidizing bacteria in soil of successional grasslands of the Drentsche A (The Netherlands). FEMS Microbiol. Ecol. 31: 207-215.
19. Kowalchuk, G.A., Buma, D.S., de Boer, W.d., Klinkhamer, P.G., and van Veen, J.A. 2002. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek, 81: 509-520.
20. Lane, D. 1991. 16S/23S rRNA sequencing. In Nucleic acid techniques in bacterial systematics. Edited by E. Stackebrandt and M. Goodfellow. John Wiley and Sons, New York. pp. 115-175.
21. Mahne, I., and Tiedje, J.M. 1995. Criteria and methodology for identifying respiratory denitrifiers. Appl. Environ. Microbiol. 61: 1110-1115.
22. Munch, J. 1991. Nitrous oxide emission from soil as determined by the composition of denitrifying microbial population. In Diversity of environmental biogeochemistry. Edited by J. Berthelin. Elsevier, Amsterdam, Netherlands, pp. 309-316.
23. Philippot, L. 2002. Denitrifying genes in bacterial and archeal genomes. Biochim. Biophys. Acta, 1577: 355-376.
24. Philippot, L., Piutti, S., Martin-Laurent, F., Hallet, S., and Germon, J.C. 2002. Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Appl. Environ. Microbiol. 68: 6121-6128.
25. Poly, F., Ranjard, L., Nazaret, S., Gourbiere, F., and Monrozier, L. 2001. Comparison of nifH gene pools in soils and soil microenvironmments with contrasting properties. Appl. Environ. Microbiol. 67: 2255-2262.
26. Prade, K., and Trolldenier, G. 1988. Effect of wheat roots on denitrification at varying soil air-filled porosity and organic-carbon content. Biol. Fertil. Soils, 7: 1-6.
27. Rosch, C., Mergel, A., and Bothe, H. 2002. Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Environ. Microbiol. 68: 3818-3829.
28. Rovira, A.D., and Dougall, B.M.M. 1967. Microbiological and biochemical aspects of the rhizosphere, In Soil biochemistry. Edited by A.D. McLaren and G.H. Petersen. Marcel Dekker, New York. pp. 417-463.
29. Scala, D.J., and Kerkhof, L.J. 1998. Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 162(1): 61-68.
30. Scala, D.J., and Kerkhof, L.J. 1999. Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 65(4): 1681-1687.
31. Shoun, H., Kano, M., Baba, I., and Takaya, N. 1998. Denitrification by actinomycetes and purification of dissimilatory nitrite reductase and azurin from Streptomyces thioluteus. J. Bacteriol. 180: 4413-4415.
32. Simpson, E.H. 1949. Measurement of diversity. Nature (London), 163: 688.
33. Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H., and Berg, G. 2001. Bulk and rhizosphere soil baterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67: 4742-4751.
34. Tan, Z., Hurek, T., and Reinhold-Hurek, B. 2003. Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ. Microbiol. 5: 1009-1015.
35. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
36. Ueda, T., Suga, Y., Yahiro, N., and Matsugushi, T. 1995. Remarkable N2 fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J. Bacteriol. 177: 1414-1417.
37. von Berg, K.L., and Bothe, H. 1992. The distribution of denitrifying bacteria in soils monitored by DNA probing. FEMS Microbiol. Ecol. 86: 331-340.
38. Weier, K.L., and MacRae, I.C. 1992. Denitrifying bacteria in the profile of a Brigalow clay soil beneath a permanent pasture and a cultivated crop. Soil Biol. Biochem. 24: 919-923.
39. Winther, F., Eiland, F., Lind, A.-M., and Elsgaard, L. 1999. Microbial biomass and numbers of denitrifiers related to macropore channels in agricultural and forest soils. Soil Biol. Biochem. 31: 603-611.
40. Xu, L.-H., Li, Q.-R., and Jiang, C.-L. 1996. Diversity of soil actinomycetes in Yunnan, China. Appl. Environ. Microbiol. 62: 244-248.
41. Zehr, J., Jenkins, B., Short, S., and Stewart, G. 2003. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5: 539-554.
42. Zumft, W. G. 1997. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61(4): 533-616.