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Impact of Long-Term Fertilization on the Composition of Denitrifier Communities Based on Nitrite Reductase Analyses in a Paddy Soil

  • Soil Microbiology
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Abstract

The effect of long-term fertilization on soil-denitrifying communities was determined by measuring the abundance and diversity of the nitrite reductase genes nirK and nirS. Soil samples were collected from plots of a long-term fertilization experiment started in 1990, located in Taoyuan (110°72″ E, 28°52″ N), China. The treatments were no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). The abundance, diversity, and composition of the soil-denitrifying bacteria were determined by using real-time quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of nirK and nirS genes. There was a pronounced difference in the community composition and diversity of nirK-containing denitrifiers responding to the long-term fertilization regimes; however, less variation was observed in communities of nirS-containing denitrifiers, indicating that denitrifiers possessing nirK were more sensitive to the fertilization practices than those with nirS. In contrast, fertilization regimes had similar effects on the copy numbers of nirK and nirS genes. The BMR treatment had the highest copy numbers of nirK and nirS, followed by the two mineral fertilization regimes (UR and BM), and the lowest was in the NF treatment. Of the measured soil parameters, the differences in the community composition of nirK and the abundance of nir denitrifiers were highly correlated with the soil carbon content. Therefore, long-term fertilization resulted in a strong impact on the community structure of nirK populations only, and total organic carbon was the dominant factor in relation to the variations of nir community sizes.

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Acknowledgements

This work was supported by the projects of KZCX2-YW-BR-01 NSFC40771115 and KZCX2-YW-423.

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Authors and Affiliations

  1. Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China

    Zhe Chen, Xiqian Luo, Minna Wu, Jinshui Wu & Wenxue Wei

  2. Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

    Zhe Chen

  3. College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China

    Xiqian Luo & Ronggui Hu

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  1. Zhe Chen
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Correspondence to Wenxue Wei.

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Table S1

Information of the selected protein sequences of nitrite reductase (coded by nirK and nirS) from GenBank, including the accession numbers and the names of strains (DOC 66 kb)

Table S2

Bacterial strains used in this study to test the specificity of the nirK and nirS primers (DOC 73 kb)

Table S3

Diversity parameters from the T-RFLP profile analysis of nirK and nirS gene fragments amplified from different fertilization practices (DOC 52 kb)

Fig. S1

Standard curves for nirK (a) or nirS (b) assays obtained by plotting the concentration of plasmid DNA versus the threshold cycle. Red multiple sign present the amplification and quantity of soil samples (DOC 124 kb)

Fig. S2

Melt curves for nirK (a) or nirS (b) gene. The Y-axis is the derivative of the slope of the signal intensity as temperature increases (DOC 365 kb)

Fig. S3

Relative abundances of nirK (a) and nirS (b) T-RFs from triplicate plots of long-term fertilization treatments. The relative abundance of T-RFs is given as a percentage of the total peak height. Fragment sizes within the graph indicate the sizes (bp) of the experimental T-RFs by T-RFLP (DOC 692 kb)

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Chen, Z., Luo, X., Hu, R. et al. Impact of Long-Term Fertilization on the Composition of Denitrifier Communities Based on Nitrite Reductase Analyses in a Paddy Soil. Microb Ecol 60, 850–861 (2010). https://doi.org/10.1007/s00248-010-9700-z

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  • DOI: https://doi.org/10.1007/s00248-010-9700-z

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