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

Haimin Chen,Zongsuo Liang,Hongxia Wu,Haihua Zhang,Fang Miao,Bin Yan,Qing Sheng,Fenghua Liu,Hongguang Zhao

doi:10.3390/ijms19030672

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.

Highlights

Seed production is one of the most important stages of plant life history
Deciphering the core microbiome across different cultivated S. miltiorrhiza seeds indicated that seed microbiome is a distinctive genetic resource for the host plant
Some studies had indicated seed microbiomes have significant impacts on host plant health and productivity [1,2,16,17,18], our study provides the first insights into the seed-associated core microbiome of a medicinal plant

Summary

Introduction

Seed production is one of the most important stages of plant life history. Seeds harbor high diversity of microbial taxa, known as seed-associated microbiomes, which are the endophytic or epiphytic microbial communities associated with seeds. The concept of core microbiome was firstly established for human microbiome, and further expanded to other host-associated microbiomes such as plants. This concept was even used to describe microbial members shared across soils, lakes, and wastewater [4,5,6]. Several studies showed that soil types and host plant genotypes are the main factors affecting the microbial community assemblage [5,7,8,9,10,11]. Studies on human microbiomes showed that human association of microbial communities have a huge impact on host metabolism [12,13,14], but few studies have analyzed the effects of plant microbiome on host metabolism. Seed microbiomes have diverse seed–microbe interactions, and properties, such as being fast-growing, use as bio-fertilizer, antagonistic properties, and ability to cope with environmental stress [17,18,19,20,21,22,23], and are predicted to be an important biological resource for sustainable agriculture [24]

Methods

Results

Conclusion