Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii

Luo, Jipeng; Tao, Qi; Wu, Keren; Li, Jinxing; Qian, Jie; Liang, Yongchao; Yang, Xiaoe; Li, Tingqiang

doi:10.1007/s00253-017-8469-0

Applied microbial and cell physiology
Published: 11 September 2017

Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii

Jipeng Luo¹,
Qi Tao¹,
Keren Wu¹,
Jinxing Li¹,
Jie Qian²,
Yongchao Liang¹,
Xiaoe Yang¹ &
Tingqiang Li¹

Applied Microbiology and Biotechnology volume 101, pages 7961–7976 (2017)Cite this article

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Abstract

Interactions between roots and microbes affect plant’s resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation.

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Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (41271333, 21477104, 41671315) and the National Key Research and Development Projects of China (2016YFD0800802). We wish to express our warm thanks to Prof. Dr. Hans Lambers of the University of Western Australia for his instructive comments on and critical reading of this manuscript. We thank the anonymous reviewers for their valuable comments and suggestions.

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Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
Jipeng Luo, Qi Tao, Keren Wu, Jinxing Li, Yongchao Liang, Xiaoe Yang & Tingqiang Li
School for Marine Sciences, Ningbo University, Ningbo, China
Jie Qian

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Jipeng Luo
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Qi Tao
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Keren Wu
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Jinxing Li
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Jie Qian
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Yongchao Liang
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Xiaoe Yang
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Tingqiang Li
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Contributions

T.L. designed the study; J.L. and Q.T. contributed equally to the manuscript; Q.T., K.W., J.L., and J.Q. performed the sample collection and laboratory work; J.L. and Q.T. analyzed the data; J.L. wrote the paper.

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Correspondence to Tingqiang Li.

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Luo, J., Tao, Q., Wu, K. et al. Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii . Appl Microbiol Biotechnol 101, 7961–7976 (2017). https://doi.org/10.1007/s00253-017-8469-0

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Received: 21 February 2017
Revised: 08 July 2017
Accepted: 30 July 2017
Published: 11 September 2017
Issue Date: November 2017
DOI: https://doi.org/10.1007/s00253-017-8469-0

Keywords

Heavy metals
Hyperaccumulator
Root-associated microbiome
Metagenome functions
Sedum alfredii