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Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng

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      Abstract

      BackgroundBacterial endophytes are widespread inhabitants inside plant tissues that play crucial roles in plant growth and biotransformation. This study aimed to offer information for the exploitation of endophytes by analyzing the bacterial endophytes in different parts of Panax notoginseng.MethodsWe used high-throughput sequencing methods to analyze the diversity and composition of bacterial endophytes from different parts of P. notoginseng.ResultsA total of 174,761 classified sequences were obtained from the analysis of 16S ribosomal RNA in different parts of P. notoginseng. Its fibril displayed the highest diversity of bacterial endophytes. Principal coordinate analysis revealed that the compositions of the bacterial endophytes from aboveground parts (flower, leaf, and stem) differed from that of underground parts (root and fibril). The abundances of Conexibacter, Gemmatimonas, Holophaga, Luteolibacter, Methylophilus, Prosthecobacter, and Solirubrobacter were significantly higher in the aboveground parts than in the underground parts, whereas the abundances of Bradyrhizobium, Novosphingobium, Phenylobacterium, Sphingobium, and Steroidobacter were markedly lower in the aboveground parts.ConclusionsOur results elucidated the comprehensive diversity and composition profiles of bacterial endophytes in different parts of 3-year-old P. notoginseng. Our data offered pivotal information to clarify the role of endophytes in the production of P. notoginseng and its important metabolites.Electronic supplementary materialThe online version of this article (10.1186/s13020-018-0198-5) contains supplementary material, which is available to authorized users.

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          The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production. Copyright © 2012 Elsevier Ltd. All rights reserved.
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            Author and article information

            Affiliations
            [1 ]ISNI 0000 0004 0632 3409, GRID grid.410318.f, Institute of Chinese Materia Medica, , China Academy of Chinese Medical Sciences, ; Beijing, 100700 China
            [2 ]Wenshan Miaoxaing Notoginseng Technology, Co., Ltd., Wenshan, 663000 China
            [3 ]ISNI 0000 0004 1756 0485, GRID grid.460126.7, Institute of Sanqi Research, , Wenshan University, ; Wenshan, 663000 China
            [4 ]GRID grid.443651.1, College of Agriculture, , Ludong University, ; Yantai, 264025 China
            Contributors
            lldong@icmm.ac.cn
            rycheng@icmm.ac.cn
            425113948@qq.com
            weifugang@live.com
            874101744@qq.com
            jxu@icmm.ac.cn
            ws-wangyong37@163.com
            guoxtina@126.com
            panaxnotoginseng@126.com
            0086-10-57203877 , slchen@icmm.ac.cn
            Journal
            Chin Med
            Chin Med
            Chinese Medicine
            BioMed Central (London )
            1749-8546
            14 August 2018
            14 August 2018
            2018
            : 13
            6092820
            198
            10.1186/s13020-018-0198-5
            © The Author(s) 2018

            Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

            Funding
            Funded by: the Fundamental Research Funds for the Central public welfare research institutes
            Award ID: ZXKT17049
            Award Recipient :
            Funded by: FundRef http://dx.doi.org/10.13039/501100005090, Beijing Nova Program;
            Award ID: Z181100006218020
            Award Recipient :
            Funded by: the Major Science and Technology Programs in Yunnan Province
            Award ID: 2016ZF001-001
            Award Recipient :
            Funded by: the Science and Technology Project of Yantai
            Award ID: 2015ZH071
            Award Recipient :
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            Research
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            © The Author(s) 2018

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