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Int. J. Mol. Sci. 2018, 19(3), 672; https://doi.org/10.3390/ijms19030672

Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?

1
College of Life Sciences, Northwest A&F University, Yangling 712100, China
2
College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
3
Tianjin Tasly Holding Group Co., Ltd., Tianjin 300410, China
*
Authors to whom correspondence should be addressed.
Received: 25 January 2018 / Revised: 21 February 2018 / Accepted: 23 February 2018 / Published: 27 February 2018
(This article belongs to the Special Issue Plant Microbe Interaction 2017)
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Abstract

Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants. View Full-Text
Keywords: seed-associated microbiome; 16S rRNA and ITS2 gene amplicons; Illumina sequencing; diversity; PICRUSt; Salvia miltiorrhiza Bge seed-associated microbiome; 16S rRNA and ITS2 gene amplicons; Illumina sequencing; diversity; PICRUSt; Salvia miltiorrhiza Bge
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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. (CC BY 4.0).

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Chen, H.; Wu, H.; Yan, B.; Zhao, H.; Liu, F.; Zhang, H.; Sheng, Q.; Miao, F.; Liang, Z. Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism? Int. J. Mol. Sci. 2018, 19, 672.

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