Molecular detection and quantification of nifH gene sequences in the rhizosphere of sorghum (Sorghum bicolor) sown with two levels of nitrogen fertilizer

Applied Soil Ecology

Volumn 42, Issue 1, 2009, Pages 48-53

  Coelho, Marcia R R ^a,b   Marriel, Ivanildo E ^c   Jenkins, Sasha N ^b   Lanyon, Clare V ^b   Seldin, Lucy ^a   O'Donnell, Anthony G ^b  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c EMBRAPA MILHO E SORGO   (Brazil)

Author keywords

DGGE; Diazotrophs; nifH gene; Real time PCR; Sorghum bicolor

Indexed keywords

BOVINE RESPIRATORY SYNCYTIAL VIRUS; RHIZOBIALES; SORGHUM BICOLOR;

EID: 62549149804     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2009.01.010     Document Type: Article

References (39)

1. Bagwell C.E., and Lovell C.R. Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability. Appl. Environ. Microbiol. 66 (2000) 4625-4633
2. Bowen G.D., and Rovira A.D. In: Waisel Y., Eschel A., and Kafkafi U. (Eds). Plant Roots: The Hidden Half (1991), Marcel Dekker, New York 349-388
3. 2 reveals novel noncultivated diazotrophs in soil. Appl. Environ. Microbiol. 73 (2007) 3196-3204
4. Carelli M., Gnocchi S., Francelli S., Mengoni A., Paffetti D., Scotti C., and Bazzicalupo M. Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfafa cultivars in Italian soils. Appl. Environ. Microbiol. 66 (2000) 4785-4789
5. Chaintreuil C., Giraud E., Prin Y., Lorquin J., Bâ A., Gillis M., de Lajudie P., and Dreyfus B. Photosynthetic Bradyrhizobia are natural entophytes of the African wild rice Oryza breviligulata. Appl. Environ. Microbiol. 66 (2000) 5437-5447
6. Church M.J., Jenkins B.D., Karl D.M., and Zehr J.P. Vertical distributions of nitrogen-fixing phylotypes at Stn ALOHA in the oligotrophic North Pacific Ocean. Aquat. Microb. Ecol. 38 (2005) 3-14
7. Church M.J., Short C.M., Jenkins B.D., Karl D.M., and Zehr J.P. Temporal patterns of nitrogenase (nifH) gene expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 71 (2005) 5362-5370
8. Coelho M.R.R., de Vos M., Carneiro N.P., Marriel I.E., Paiva E., and Seldin L. Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol. Lett. 279 (2008) 15-22
9. Coelho M.R.R., Mota F.F., Carneiro N.P., Marriel I.E., Paiva E., Rosado A.S., and Seldin L. Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer accessed by rpoB-based PCR-DGGE and sequencing analysis. J. Microbiol. Biotechnol. 17 (2007) 753-760
10. Deslippe J., and Egger K. Molecular diversity of nifH genes from bacteria associated with high arctic dwarf shrubs. Microb. Ecol. 51 (2006) 516-525
11. 2-fixing bacterial diversity in soil under Acacia tortilis ssp. raddiana and Balanites aegyptiaca in the dryland part of Senegal. Environ. Microbiol. 6 (2004) 400-415
12. 15N isotope dilution technique. Biol. Fertil. Soils 23 (1996) 249-256
13. Gray N.D., and Head I.M. Linking genetic identity and function in communities of uncultured bacteria. Environ. Microbiol. 3 (2001) 481-492
14. Griffiths R.I., Whiteley A.S., O'Donnell A.G., and Bailey M.J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66 (2000) 5488-5491
15. Gutierrez-Zamora M.L., and Martinez-Romero E. Natural endophytic association between Rhizobium etli and maize (Zea mays L.). J. Biotechnol. 91 (2001) 117-126
16. Izquierdo J.A., and Nusslein K. Distribution of extensive nifH gene diversity across physical soil microenvironments. Microb. Ecol. 51 (2006) 441-452
17. Juraeva D., George E., Davranov K., and Ruppel S. Detection and quantification of the nifH gene in shoot and root of cucumber plants. Can. J. Microbiol. 52 (2006) 731-739
18. Kanungo P.K., Kamakrishnan B., and Rao V.R. Placement effects of organic sources on nitrogenase activity and nitrogen-fixing bacteria in flooded rice soils. Biol. Fertil. Soils 25 (1997) 103-108
19. Knauth S., Hurek T., Brar D., and Reinhold-Hurek B. Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice. Environ. Microbiol. 7 (2005) 1725-1733
20. Lovell C.R., Piceno Y.M., Quattro J.M., and Bagwell C.E. Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl. Environ. Microbiol. 66 (2000) 3814-3822
21. Mergel A., Schmitz O., Mallmann T., and Bothe H. Relative abundance of denitrifiying and dinitrogen-fixing bacteria in layers of a forest soil. FEMS Microbiol. Ecol. 36 (2001) 33-42
22. Peoples M.B., and Craswell E.T. Biological nitrogen fixation: investments, expectations and actual contributions to agriculture. Plant Soil 141 (1992) 13-39
23. Piceno Y.M., and Lovell C.R. Stability in natural bacterial communities. I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb. Ecol. 39 (2000) 32-40
24. Poly F., Monrozier L.J., and Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res. Microbiol. 152 (2001) 95-103
25. Poly F., Ranjard L., Nazaret S., Gourbière F., and Monrozier L.J. Comparison of nifH gene pools in soil and soil microenvironments with contrasting properties. Appl. Environ. Microbiol. 67 (2001) 2255-2262
26. Roesch L.F.W., Olivares F.L., Passaglia L.M.P., Selbach P.A., Saccol de Sa E.L., and Oliveria de Camargo F.A. Characterization of diazotrophic bacteria associated with maize: effect of plant genotype, ontogeny and nitrogen supply. World J. Microbiol. Biotechnol. 22 (2006) 967-974
27. Short S.M., and Zehr J.P. Quantitative analysis of nifH genes and transcripts from aquatic environments. Methods Enzymol. 397 (2005) 380-394
28. Simonet P., Grojean M.C., Misra A.K., Nazaret S., Cournoyer B., and Normand P. Frankia genus-specific characterization by polymerase chain reaction. Appl. Environ. Microbiol. 57 (1991) 3278-3286
29. Tan Z., Hurek T., and Reinhold-Hurek B. Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ. Microbiol. 5 (2003) 1009-1015
30. Tate R.L. Nitrogen fixation. In: Tate R.L. (Ed). The Gateway to Soil Nitrogen Cycling (1995), John Wiley and Sons, Inc., Hoboken, NJ, USA 283-306
31. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J. Bacteriol. 177 (1995) 1414-1417
32. Wallenstein M.D., and Vilgalys R.J. Quantitative analyses of nitrogen cycling genes in soils. Pedobiologia 49 (2005) 665-672
33. Wartiainen I., Eriksson T., Zheng W., and Rasmussen U. Variation in the active diazotrophic community in rice paddy-nifH PCR-DGGE analysis of rhizosphere and bulk soil. Appl. Soil Ecol. 39 (2008) 65-75
34. Widmer F., Shaffer B.T., Porteous L.A., and Seidler R.J. Analysis of nifH gene pool complexity in soil and litter at Douglas fir forest site in the Oregon cascade mountain range. Appl. Environ. Microbiol. 65 (1999) 374-380
35. Wu L., Ma K., and Lu Y. Prevalence of Betaproteobacterial sequences in nifH gene pools associated with roots of modern rice cultivars. Microb. Ecol. 57 (2009) 58-68
36. Yanni Y.G., Rizk1 R.Y., Corich V., Squartini A., Ninke K., Philip-Hollingsworth S., Orgambide G., de Bruijn F., Stoltzfus J., Buckley D., Schmidt T.M., Mateos P.F., Ladha J.K., and Dazzo F.B. Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. Plant Soil 194 (1997) 99-114
37. Young J.P.W. Phylogenetic classification of nitrogen-fixing organisms. In: Stacey G., Burris R.H., and Evans H.J. (Eds). Biological Nitrogen Fixation (1992), Chapman and Hall, New York, NY 43-86
38. Zehr J.P., Jenkins B.D., Short S.M., and Steward G.F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5 (2003) 539-554
39. Zhang Y., Li D., Wang H., Xiao Q., and Liu X. Molecular diversity of nitrogen-fixing bacteria from the Tibetan Plateau, China. FEMS Microbiol. Lett. 260 (2006) 134-142