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Genetic diversity analysis of diazotrophs in the rice rhizosphere

Published online by Cambridge University Press:  13 February 2008

Chen Bin ,
Zheng Si-Ping ,
Zhou Li-Juan ,
Lin Zhi-Min ,
Song Ya-Na  and
Zheng Wei-Wen
Chen Bin
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
Zheng Si-Ping
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
Zhou Li-Juan
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
Lin Zhi-Min
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
Song Ya-Na
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
Zheng Wei-Wen*
Affiliation:
Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
*
*Corresponding author. E-mail: [email protected]
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Summary

The genetic diversity of dinitrogen-fixing bacteria associated with rice (Oryza sativa) was assessed by a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach on the nifH gene amplified directly from DNA extracted from washed rice roots and rhizospheric soil. Restriction digestion with the enzymes MnlI and HaeIII was performed to characterize 54 cloned nifH PCR products. RFLP profiles were clustered and analysed with the UPGMA program. Eight pairs of similar RFLP patterns (similarity>50%) and two pairs of homologous RFLP patterns (100% identity) were found from the washed roots and the rhizospheric soil, respectively. Three specific diazotrophic patterns were found from rhizospheric soil and rice roots. The analyses have revealed the presence of different nifH types, which appear to be significant components of the diazotrophic community in paddy fields, indicating that some of the diazotrophs may colonize the inside and the surface of the rice roots.

Keywords

nifHpolymerase chain reactionrestriction fragment length polymorphismricerhizospheric soil
Type
Research Article
Information
Chinese Journal of Agricultural Biotechnology , Volume 4 , Issue 3 , December 2007 , pp. 253 - 258
Copyright
Copyright © China Agricultural University and Cambridge University Press 2007

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Footnotes

First published in Journal of Agricultural Biotechnology 2007, 15(5): 841–846

References

Barraquio, WL, Revilla, L and Ladha, JK (1997) Isolation of endophytic diazotrophic bacteria from wetland rice. Plant Soil 194: 15–24.CrossRefGoogle Scholar
Boddey, RM (1995) Biological nitrogen fixation in sugar cane: a key to energetically viable biofuel production. Critical Reviews in Plant Science 14: 263–279.CrossRefGoogle Scholar
Bodelier, PLE (2003) Interaction between oxygen-releasing roots and microbial processes in flooded soils and sediments. Ecology Studies 168: 331–362.CrossRefGoogle Scholar
Buergmann, H, Widmer, F, von Sigler, W and Zeyer, J (2004) New molecuLar screening tools for analysis of free-living diazotrophs in soil. Applied and Environmental Microbiology 70: 240–270.CrossRefGoogle Scholar
Egener, T, Hurek, T and Reinhold-Hurek, B (1999) Endophytic expression of nif genes of Azoarcus sp. strain BH72 in rice roots. Molecular Plant–Microbe Interactions 12: 813–819.CrossRefGoogle Scholar
Engelhard, M, Hurek, T and Reinhold-Hurek, B (2000) Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild species and land races of Oryza sativa in comparison with modern races. Applied and Environmental Microbiology 2: 131–141.Google ScholarPubMed
Hurek, T, Reinhold-Hurek, B, van Montagu, M and Kellenberger, E (1994) Root colonization and systemic spreading of Azoarcus sp. strain Bh72 in grasses. Journal of Bacteriology 176: 1913–1923.CrossRefGoogle ScholarPubMed
Hurek, T, Egener, T and Reinhold-Hurek, B (1997) Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β-subclass. Journal of Bacteriology 179: 4172–4178.CrossRefGoogle ScholarPubMed
Hurek, T, Handley, L, Reinhold-Hurek, B and Piche, Y (2002) Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state. Molecular Plant–Microbe Interactions 15: 233–242.CrossRefGoogle Scholar
Hurt, RA, Qiu, X, Wu, L, et al. (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Applied and Environmental Microbiology 67(10): 4495–4503.CrossRefGoogle ScholarPubMed
James, EK and Olivares, FL (1998) Infection and colonization of sugar cane and other graminaceous plants by endophytic diazotrophs. Critical Reviews in Plant Science 17: 77–119.CrossRefGoogle Scholar
James, EK, Gyaneshwar, P, Mathan, N, et al. (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Molecular Plant–Microbe Interactions 15: 894–906.CrossRefGoogle ScholarPubMed
Knauth, S, Hurek, T, Brar, D and Reinhold-Hurek, B (2005) Influence of difference Oryza cultivars on expression of nifH gene pools in roots of rice. Environmental Microbiology 7(11): 1725–1733.CrossRefGoogle ScholarPubMed
Lotta, M (2005) Biodiversity and nifH gene expression of diazotrophs in rice paddy fields. PhD dissertation, Department of Botany, Stockholm University, Sweden.Google Scholar
Lovell, CR, Piceno, YM, Quattro, JM and Bagwell, CE (2000) Molecular analysis of diazotroph diversity in the rhizosphere of smooth cordgrass, Spartina alterniflora. Applied and Environmental Microbiology 66: 3814–3822.CrossRefGoogle ScholarPubMed
McClung, CR, van Berkum, P, Davis, RE and Sloger, C (1983) Enumeration and localization of N2-fixing bacteria associated with roots of Spartina alterniflora Loisel. Applied and Environmental Microbiology Reviews 59: 604–622.Google Scholar
Moeseneder, MM, Winter, C, Arrieta, JM and Herndl, GJ (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. Journal of Microbiology Methods 44: 159–172.CrossRefGoogle ScholarPubMed
Poly, F, Ranjard, L, Nazaret, S, Gourbiere, F and Monrozier, LJ (2001) Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Applied and Environmental Microbiology 67: 2255–2262.CrossRefGoogle ScholarPubMed
Qiu, YS, Zhou, SP and Mo, XZ (1980) Studies on diazotrophs in rice roots. Chinese Science Bulletin 25(21): 1008.Google Scholar
Reinhold, B, Hurek, T, Niemann, EG and Fendrik, I (1986) Close association of Azospirillum and diazotrophic rods with different root zones of Kallar grass. Applied and Environmental Microbiology 52: 520–526.CrossRefGoogle ScholarPubMed
Reinhold-Hurek, B and Hurek, T (1998) Life in grasses: diazotrophic endophytes. Trends in Microbiology 6: 139–144.CrossRefGoogle ScholarPubMed
Reinhold-Hurek, B, Maes, T, Gemmer, S, Van Montagu, M and Hurek, T (2006) An endoglucanase is involved in infection of rice roots by the not-cellulose-metabolizing endophyte Azoarcus sp. strain BH72. Molecular Plant–Microbe Interactions 19: 181–188.CrossRefGoogle ScholarPubMed
Song, T, Lotta, M, Torsten, E, Weiwen, Z and Ulla, R (2005) Biodiversity and seasonal variation of the cyanobacterial assemblage in a rice paddy field in Fujian. FEMS Microbiology Ecology 54: 131–140.CrossRefGoogle Scholar
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. Environmental Microbiology 5: 1009–1015.CrossRefGoogle ScholarPubMed
Ueda, T, Suga, Y, Yahiro, N and Matsuguchi, T (1995) Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. Journal of Bacteriology 177: 1414–1417.CrossRefGoogle ScholarPubMed
Young, JPW, Stacy, G, Burris, RH and Evans, HJ(editors) (1992) Biological Nitrogen Fixation, Phylogenic Classification of Nitrogen-fixing Organisms. London: Chapman & Hall. pp. 43–86.Google Scholar