Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice

Environmental Microbiology

Volumn 7, Issue 11, 2005, Pages 1725-1733

  Knauth, Stefan ^a   Hurek, Thomas ^a   Brar, Darshan ^b   Reinhold Hurek, Barbara ^a  

^a UNIVERSITY OF BREMEN   (Germany)

^b INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NITROGENASE REDUCTASE; OXIDOREDUCTASE;

ARTICLE; BACTERIUM; CLUSTER ANALYSIS; COMPARATIVE STUDY; CROSS BREEDING; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT ROOT; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; SOUTHERN BLOTTING; SPECIES DIFFERENCE;

BACTERIA; BASE SEQUENCE; BLOTTING, SOUTHERN; CLUSTER ANALYSIS; CROSSES, GENETIC; GENE EXPRESSION PROFILING; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; OXIDOREDUCTASES; PHYLOGENY; PLANT ROOTS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); ORYZA; ORYZA BRACHYANTHA; ORYZA SATIVA;

EID: 27444441768     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00841.x     Document Type: Article

References (47)

1. Armstrong, W. (1978) Root aeration in the wet land condition. In Plant Life in Anaerobic Environments. Hook, D.D., and Crawford, R.M.M. (eds). Ann Arbor, MI, USA: Ann Arbor Science Publishers, pp. 269-297.
2. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds). (1987) Current Protocols in Molecular Biology. New York, USA: John Wiley & Sons.
3. Barraquio, W.L., Revilla, L., and Ladha, J.K. (1997) Isolation of endophytic diazotrophic bacteria from wetland rice. Plant Soil 194: 15-24.
4. Begg, C.B.M., Kirk, G.J.D., Mackenzie, A.F., and Neue, H.-U. (1994) Root-induced iron oxidation and pH changes in the lowland rice rhizosphere. New Phytol 128: 469-477.
5. Boddey, R.M. (1995) Biological nitrogen fixation in sugar cane: a key to energetically viable biofuel production. Crit Rev Plant Sci 14: 263-279.
6. Bodelier, P.L.E. (2003) Interaction between oxygen-releasing roots and microbial processes in flooded soils and sediments. Ecol Studies 168: 331-362.
7. Brar, D., and Kush, G.S. (2002) Transferring genes from wild species into rice. In Quantitative Genetics, Genomics and Plant Breeding. Kang, M.S. (ed.). Wallingford, UK: CAB International, pp. 197-217.
8. Briones, A.M., Okabe, S., Umemiya, Y., Ramsing, N.B., Reichardt, W., and Okuyama, H. (2002) Influence of different cultivars on populations of ammonia-oxidizing bacteria in the root environment of rice. Appl Environ Microbiol 68: 3067-3075.
9. Bürgmann, H., Widmer, F., Sigler, W.V., and Zeyer, J. (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69: 1928-1935.
10. Cassman, K.G., De Datta, S.K., Olk, D.C., Alcantara, J.M., Samson, M.I., Descalsota, J.P., and Dizon, M.A. (1995) Yield decline and the nitrogen conomy of long-term experiments on continuous, irrigated rice systems in the tropics. In Soil Management: Experimental Basis for Sustainability and Environmental Quality. Lal, R., and Stewart, B.A. (eds). Boca Raton, FL, USA: Lewis/CRC Publishers, pp. 181-222.
11. Chang, S., Puryear, J., and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Reptr 11: 113-116.
12. Egener, T., Hurek, T., and Reinhold-Hurek, B. (1999) Endophytic expression of nif genes of Azoarcus sp. strain BH72 in rice roots. Mol Plant-Microbe In 12: 813-819.
13. Engelhard, M., Hurek, T., and Reinhold-Hurek, B. (2000) Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern races. Environ Microbiol 2: 131-141.
14. Felske, A., Wolterink, A., Van Lis, R., De Vos, W.M., and Akkermans, A.D. (2000) Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66: 3998-4003.
15. Galloway, J.N., Schlesinger, W.H., Levy, H.I., Michaels, A.F., and Schnoor, J.L. (1995) Nitrogen fixation: Anthropogenic enhancement-environmental response. Global Biogeochem Cycles 9: 235-252.
16. Gyaneshwar, P., James, E.K., Reddy, P.M., and Ladha, J.K. (2002) Herbaspirillum colonization increases growth and nitrogen accumulation in aluminium-tolerant rice varieties. New Phytol 154: 131-145.
17. Hurek, T., and Reinhold-Hurek, B. (1999) Interactions of Azoarcus sp. with rhizosphere fungi. In Mycorrhiza. Varma, A., and Hock, B. (eds). Berlin, Germany: Springer Verlag, pp. 595-614.
18. 2-fixing microbes associated with graminaceous plants. In Agriculture, Forestry, Ecology and the Environment. Werner, D., and Newton, W.E. (eds). Dordrecht, The Netherlands: Kluwer Academic Publishers (in press).
19. Hurek, T., Reinhold-Hurek, B., Van Montagu, M., and Kellenberger, E. (1994) Root colonization and systemic spreading of Azoarcus sp. strain BH72 in grasses. J Bacteriol 176: 1913-1923.
20. Hurek, T., Egener, T., and Reinhold-Hurek, B. (1997) Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β-subclass. J Bacteriol 179: 4172-4178.
21. Hurek, T., Handley, L., Reinhold-Hurek, B., and Piché, Y. (2002) Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state. Mol Plant-Microbe In 15: 233-242.
22. James, E.K., and Olivares, F.L. (1998) Infection and colonization of sugar cane and other graminaceous plants by endophytic diazotrophs. Crit Rev Plant Sci 17: 77-119.
23. Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. CABIOS 8: 275-282.
24. Karl, D., Bergman, B., Capone, D., Carpenter, E., Letelier, R., Lipschultz, F., et al. (2002) Dinitrogen fixation in the world's oceans. Biogechem 57/58: 47-98.
25. Kumar, S., Tamura, K., and Nei, M. (2004) MEGA 3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
26. 15N-aided nitrogen balance. Soil Biol Biochem 19: 165-170.
27. Lovell, C.R., Piceno, Y.M., Quattro, J.M., and Bagwell, C.E. (2000) Molecular analysis of diazotroph diversity in the rhizosphere of smooth cordgrass, Spartina alterniflora. Appl Environ Microbiol 6B: 3814-3822.
28. 2-fixing bacteria associated with roots of Spartina alterniflora Loisel. Appl Environ Microbiol 45: 1914-1920.
29. Merrick, M., and Edwards, R. (1995) Nitrogen control in bacteria. Microbiol Rev 59: 604-622.
30. Moeseneder, M.M., Winter, C., Arrieta, J.M., and Herndl, G.J. (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J Microbiol Methods 44: 159-172.
31. Noda, S., Ohkuma, M., Usami, R., Horikoshi, K., and Kudo, T. (1999) Culture-independent characterization of a gene responsible for nitrogen fixation in the symbiotic microbial community in the gut of the termite Neotermes koshunensis. Appl Environ Microbiol 65: 4935-4942.
32. Piceno, Y.M., and Lovell, C.R. (2000) Stability in natural bacterial communities. I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39: 32-40.
33. Poly, F., Ranjard, L., Nazaret, S., Gourbiere, F., and Monrozier, L.J. (2001) Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl Environ Microbiol 67: 2255-2262.
34. Reinhold, B., Hurek, T., Niemann, E.-G., and Fendrik, I. (1986) Close association of Azospirillum and diazotrophic rods with different root zones of Kallar grass. Appl Environ Microbiol 52: 520-526.
35. Reinhold-Hurek, B., and Hurek, T. (1998) Life in grasses: diazotrophic endophytes. Trends Microbiol 6: 139-144.
36. Reinhold-Hurek, B., Hurek, T., Claeyssens, M., and Van Montagu, M. (1993) Cloning, expression in Escherichia coli, and characterization of cellulolytic enzymes of Azoarcus sp., a root-invading diazotroph. J Bacteriol 175: 7056-7065.
37. Seghers, D., Top, E.M., Reheul, D., Bulcke, R., Boeckx, P., Verstraete, W., and Siciliano, S.D. (2003) Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils. Environ Microbiol 5: 867-877.
38. Seghers, D., Wittebolle, L., Top, E.M., Verstraete, W., and Siciliano, S.D. (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol 70: 1475-1482.
39. Shrestha, R.K., and Ladha, J.K. (1996) Genotypic variation in promotion of rice dinitrogen fixation as determined by nitrogen-15 dilution. Soil Sci Soc Am J 60: 1815-1821.
40. 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.
41. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
42. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177: 1414-1417.
43. Valdés, M., Perez, N.-O., Estrada-de los Santos, P., Caballero-Mellado, J., Pena-Cabriales, J.J., Normand, P., and Hirsch, A.M. (2005) Non-Frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen. Appl Environ Microbiol 71: 460-466.
44. Van de Peer, Y., and de Wachter, R. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10: 569-570.
45. 2- fixation on the rhizosphere by irrigated rice plants. Theoret Appl Genet 91: 1177-1183.
46. Zehr, J.P., and McReynolds, L.A. (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55: 2522-2526.
47. Zehr, J.P., Jenkins, B.D., Short, S.M., and Steward, G.F. (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5: 539-554.