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Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing

  • Soil Microbiology
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Abstract

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

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Acknowledgments

This study was financially supported by the 973 project (2015CB150500), Innovative Research Team Development Plan of the Ministry of Education of China (IRT1256), and National Natural Science Foundation of China (no. 31201683). We would like to thank Personal Biotechnology Company (Shanghai, China) for their help with the pyrosequencing experiments and Spice and Beverage Research Institute (Wanning, China) for huge help to us in vanilla planting.

Conflict of Interest

We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work.

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Authors and Affiliations

  1. National Engineering Research Center for Organic-based Fertilizers, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China

    Wu Xiong, Jun Zhao, Weibing Xun, Rong Li, Ruifu Zhang & Qirong Shen

  2. Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China

    Wu Xiong, Qingyun Zhao & Huasong Wu

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  1. Wu Xiong
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Correspondence to Qirong Shen.

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Fig. S1

Average relative abundance (%) of bacterial and fungal phyla in 4 time-series soil from vanilla fields. The “others” comprised the rare bacterial/fungal phyla (RA <0.1 %). (GIF 4 kb)

High Resolution Image (TIFF 1267 kb)

Fig. S2

Venn diagrams showed shared unique OTUs of bacteria and fungi in the soils from 4 time-series vanilla fields. “a”, “b”, “c” and “d” represent field with 1, 6, 11 or 21 years continuous cropping history, respectively. (GIF 3 kb)

High Resolution Image (TIFF 1375 kb)

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Xiong, W., Zhao, Q., Zhao, J. et al. Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing. Microb Ecol 70, 209–218 (2015). https://doi.org/10.1007/s00248-014-0516-0

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