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Volume 19
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10.3390/ijms19082394
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Article

Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture

by
Linkun Wu
1,2,
Juanying Wang
1,2,
Hongmiao Wu
1,2,
Jun Chen
1,2,
Zhigang Xiao
1,2,
Xianjin Qin
2,3,
Zhongyi Zhang
3,4 and
Wenxiong Lin
2,3,*
1
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou 350002, China
3
Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China
4
College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(8), 2394; https://doi.org/10.3390/ijms19082394
Received: 21 July 2018 / Revised: 8 August 2018 / Accepted: 8 August 2018 / Published: 14 August 2018
(This article belongs to the Section Biochemistry)
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Abstract

Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture. View Full-Text
Keywords: Rehmannia glutinosa; soil sickness; metagenomics; rhizosphere microbiome; functional potential Rehmannia glutinosa; soil sickness; metagenomics; rhizosphere microbiome; functional potential
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

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MDPI and ACS Style

Wu, L.; Wang, J.; Wu, H.; Chen, J.; Xiao, Z.; Qin, X.; Zhang, Z.; Lin, W. Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture. Int. J. Mol. Sci. 2018, 19, 2394. https://doi.org/10.3390/ijms19082394

AMA Style

Wu L, Wang J, Wu H, Chen J, Xiao Z, Qin X, Zhang Z, Lin W. Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture. International Journal of Molecular Sciences. 2018; 19(8):2394. https://doi.org/10.3390/ijms19082394

Chicago/Turabian Style

Wu, Linkun; Wang, Juanying; Wu, Hongmiao; Chen, Jun; Xiao, Zhigang; Qin, Xianjin; Zhang, Zhongyi; Lin, Wenxiong. 2018. "Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture" Int. J. Mol. Sci. 19, no. 8: 2394. https://doi.org/10.3390/ijms19082394

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