Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species.

Jianbo Xie,Haowen Shi,Zhenglin Du,Xiaomeng Liu,Tianshu Wang,Sanfeng Chen

doi:10.1038/srep21329

Abstract

Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.

Highlights

Our lab has completed genome sequencing of 13 nitrogen-fixing Paenibacillus spp., including P. polymyxa strains WLY78, TD94 and 1–43 and other nitrogen fixers of this genus[17,18,19]
The phylogenetic trees, inferred with Bayesian inference (BI) and Neighbour-joining (NJ) methods (Figs S1 and S2), are congruent with the Maximum likelihood (ML) phylogenetic tree. These trees show that the 9 P. polymyxa strains (WLY78, 1–43, TD94, E681, SC2, ICGEB 2008, M1, OSY-DF, ATCC 842) and the other strains
P. polymyxa strains have long been known for their ability to produce peptide antibiotics, such as polymyxins, polypeptins, gavaserin, saltavalin, gatavalin and fusaricidin

Summary

Introduction

Our lab has completed genome sequencing of 13 nitrogen-fixing Paenibacillus spp., including P. polymyxa strains WLY78, TD94 and 1–43 and other nitrogen fixers of this genus[17,18,19]. We compared these strains to each other and to 18 other strains (2 N2-fixing strains and 16 non-N2-fixing strains) and revealed the heterogeneity, organization and evolution of the nitrogen fixation genes within the 31 genomes. This study reveals the genome architecture and evolution of the genus Paenibacillus, and provides an in-depth understanding of plant-growth promoting traits of P. polymyxa and its closely related species

Methods

Results

Conclusion