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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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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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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DOI: https://doi.org/10.1007/s00253-017-8469-0