Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance

Abstract

Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.

Keywords: auxin; endophytic bacteria; genome mining; phylogenomics; plant growth promotion; plant-microbe interaction.

FIGURE 1

Effect of Stenotrophomonas strain 169 on the performance of the in vitro poplar clone 741 in comparison to that of the uninoculated control 4 weeks after inoculation. Differences in root and shoot length as well as the number of roots are shown in the bar charts. Stars indicate significant differences (p < 0.001, Wilcoxon rank sum test), vertical error bars display standard error.

FIGURE 2

Effects of strain 169 on root and shoot development of the hybrid poplar clone 741 in vitro. All measured parameters were significantly increased in the inoculated plants (p < 0.0001, Wilcoxon rank sum test).

FIGURE 3

Comparison of orthologous genes between the genomes of Stenotrophomonas sp. 169, S. chelatiphaga DSM 21508^T, S. rhizophila DSM 14405^T, and S. maltophilia R551-3. The number of shared and genome-specific genes is shown.

FIGURE 4

Phylogenomic tree showing the position of Stenotrophomonas sp. 169 among type strains and other reference strains of closely related Stenotrophomonas species. Xanthomonas campestris and Xanthomonas gardneri were used as outgroup. The maximum-likelihood tree is based on concatenated 120 core marker proteins. Numbers at branch nodes refer to bootstrap values > 70%. Bar: amino acid substitutions per position. Assembly accession numbers are indicated in brackets.

FIGURE 5

Spermidine biosynthesis pathway found in Stenotrophomonas sp. 169. The scheme is based on Jelsbak et al. (2014) and Xie et al. (2014). Blue arrows indicate genes found in the genome of strain 169.

FIGURE 6

Overview of the bacterial IAA biosynthetic pathways adapted from Spaepen and Vanderleyden (2011). Blue arrows indicate the presence of enzymes detected in Stenotrophomonas sp. 169: (1) amidase AmiE, EC 3.5.1.4, (2) aldehyde dehydrogenase, EC 1.2.1.3, (3) indole-pyruvate ferredoxin oxidoreductase, EC 1.2.7.8.