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

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.

Figure 1. Phylogenetic relationship and population structure of 35 Paenibacillus strains.

P. polymyxa strains are indicated by black circular beside the strain names. (A) ML phylogenetic tree was constructed using based on 244 single-copy core proteins shared by 35 genomes and an out-group (Bacillus cereus ATCC 10987). The phylogenetic tree was rooted by the out-group. Support values of phylogenetic tree are shown for nodes as maximum likelihood bootstrap. (B) ML phylogenetic tree of 14 strains within Poly-clade. The four subgroups are indicated by the vertical lines on the right of the phylogentic tree. (C) Analysis of population structure of 35 Paenibacillus strains and the B. cereus ATCC 10987 strain. The 36 strains were divided into 7 populations (K = 7) using STRUCTURE, which marked by brackets. Individuals are shown by thin vertical lines, which are divided into K colored segments standing for the estimated membership probabilities (Q) of each individual. Finally, all individuals are classified based on the Q-matrix. A column in a single color indicates clonal structure. A column in mixed colors indicates migrants and admixed individual.

Figure 2. Chromosome map and distribution of SNP in 14 Poly-clade strains.

From outside of circle to inside of circle. Circle 1 is gene density map (red). Circle 2 is GC content density map (green). Circle 3 is distribution of SNP (orange).

Figure 3. Functional classification of strain-specific genes in 14 Poly-clade strains.

The number in each square represents the COG assignment in each functional category. The annotated specific gene number in each functional category and the total specific gene number were listed behind Paenibacillus strain number.

Figure 4. Plant growth promoting traits of Poly-clade strains.

(A) Genes involved in nitrogen fixation and nitrogenase activities of five Paenibacillus strains. (B) Genes and activitie involved in IAA production, organic and inorganic phosphate solubilization. Colored box represents the presence of a gene within a genome and white box indicates absence of a gene.

Figure 5. Biosynthetic gene clusters and predicted structures of peptide antibiotics (Nrps or Pks) in some Poly-clade strains.

The gene product and the predicted structure were deduced by homologous blast.

Figure 6. Comparison of biosynthetic gene clusters of peptide antibiotics (NRPs or PKs) from Poly-clade strains and other bacteria.

Regions of conserved synteny were marked with grey shadow. The strains within the curved bracket shared the same gene cluster on the left of the bracket. Different genes are filled with different color, and genes with the same color are homologous to each other.