Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence

Yang Zhang,Xu Gao,Qirong Shen,Shuai Wang,Rong Li,Chengzhi Zhu

doi:10.1007/s00284-018-1563-4

Yang Zhang, Xu Gao + Show 4 more

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https://doi.org/10.1007/s00284-018-1563-4

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Journal: Current Microbiology	Publication Date: Sep 7, 2018
Citations: 16	License type: open-access

Affiliation: Utrecht University

Abstract

Plant growth-promoting rhizobacteria (PGPR) have been reported to influence plant growth, yield, and nutrient uptake by an array of mechanisms. Uncovering the behavioral dynamics of PGPR is one of the most important issues necessary for understanding their functional performances. In this study, strain NJAU-Z9 which was found to possess complex functions and efficient rhizospheric colonization ability was selected from plenty of bacterial strains isolated randomly from the pepper rhizosphere soil and identified as Bacillus velezensis. Repeated seedling nursing tests performed absolute growth-promoting advantage for the novel isolated strain. After that, primers for the quantitative detection were designed based on its whole genome sequence (WGS), and a real-time PCR method was utilized to explore strategies for monitoring the strain in natural soil and in the pepper rhizosphere. Results showed based on the whole genome, two primers were identified as NJAU-Z9-specific quantitative PCR primers. Two seasonal pot experiments demonstrated that strain NJAU-Z9 effectively colonized the rhizosphere measured by the novel abundance detecting strategy, improved plant growth, and showed a positive correlation between bacterial number and biomass. This study offers a strategy based on a real-time PCR method for directly monitoring B. velezensis strain NJAU-Z9 in the soil and the rhizosphere and provides a reference for the quantitative study of other PGPR strains based on WGSs.

Highlights

Plant growth-promoting rhizobacteria (PGPR) use one or more different mechanisms to promote plant growth and health directly or indirectly [1]
Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NJAU-Z9 belonged to the genus Bacillus and formed a subclade with B. velezensis CBMB205T and B. velezensis FZB42T (Fig. 1) with a robust bootstrap support in the maximum-likelihood tree
The Average nucleotide identity (ANI) values between NJAU-Z9 and the type strains B. velezensis CBMB205T, B. velezensis FZB42T, and B. amyloliquefaciens DSM 7 T are all greater than 94%, and B. velezensis CBMB205T is the closest one with ANI value of 97.94%

Summary

Introduction

Plant growth-promoting rhizobacteria (PGPR) use one or more different mechanisms to promote plant growth and health directly or indirectly [1]. Real-time quantitative PCR (qPCR) is widely used for the detection and quantification of 16S rRNA genes [13] and for identifying functional genes involved in rhizosphere-related processes due to its high specificity, sensitivity, and speed [14]. These reports showed that qPCR is a valuable technique for quantitatively monitoring populations of unlabeled bacteria in greenhouse experiments, utilization of strain primers leads to robust detection for target microbes. The application of strain primers is more difficult in field experiments where closely related indigenous bacteria may interfere with amplification and quantification

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