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Diazotrophic diversity, nifH gene expression and nitrogenase activity in a rice paddy field in Fujian, China

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Abstract

The diazotrophic communities in a rice paddy field were characterized by a molecular polyphasic approach including DNA/RNA-DGGE fingerprinting, real time RT-PCR analysis of nifH gene and the measurement of nitrogen fixation activities. The investigation was performed on a diurnal cycle and comparisons were made between bulk and rhizosphere / root soil as well as between fertilized / unfertilized soils. Real time RT-PCR showed no significant difference in the total quantity of nifH expression under the conditions investigated. The functional diversity and dynamics of the nifH gene expressing diazotroph community investigated using RT-PCR-DGGE revealed high diurnal variations, as well as variation between different soil types. Most of the sequence types recovered from the DGGE gels and clone libraries clustered within nifH Cluster I and III (65 different nifH sequences in total). Sequence types most similar to Azoarcus spp., Metylococcus spp., Rhizobium spp., Methylocystis spp., Desulfovibrio spp., Geobacter spp., Chlorobium spp., were abundant and indicate that these species may be responsible for the observed diurnal variation in the diazotrophic community structure in these rice field samples. Previously described diazotrophic cyanobacterial genera in rice fields, such as Nostoc and Cyanothece, were present in the samples but not detectable in RT-PCR assays.

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Acknowledgments

This work was supported by grants to UR from The Swedish International Development Cooperation Agency Department for Research Cooperation (Sida/SAREC) and The Swedish Research Link Programme. Grant from The Swedish Research Council (FORMAS) to RE is acknowledged. We also acknowledge the financial support from K. and A. Wallenberg Foundation. Dr. L. Zhou and Mr Z. Lin are acknowledged for help during the fieldwork, Ms C. Bin for help during fieldwork and DGGE experiments and Ms S. Vintila, Department of Botany, Stockholm University, for help with statistical analyses.

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Authors and Affiliations

  1. Department of Botany, Stockholm University, SE-106 91, Stockholm, Sweden

    Lotta Mårtensson, Beatriz Díez, Ingvild Wartiainen, Rehab El-Shehawy & Ulla Rasmussen

  2. Biotechnology Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, Peoples Republic of China

    Weiwen Zheng

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  1. Lotta Mårtensson
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  2. Beatriz Díez
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  3. Ingvild Wartiainen
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  6. Ulla Rasmussen
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Correspondence to Ulla Rasmussen.

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Responsible Editor: Euan K. James.

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Mårtensson, L., Díez, B., Wartiainen, I. et al. Diazotrophic diversity, nifH gene expression and nitrogenase activity in a rice paddy field in Fujian, China. Plant Soil 325, 207–218 (2009). https://doi.org/10.1007/s11104-009-9970-8

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