Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

Abstract

Background: The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4.

Results: Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms.

Conclusion: The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants.

Keywords: Beachgrass; Comparative genomics; PGPR; Rhizobacterium; Sphingobium.

Fig. 1

Plant-growth promotion assays using Arabidopsis and switchgrass inoculated with Sphingobium sp. strain AEW4 or uninoculated controls. Changes in root biomass were measured as increase in length for Arabidopsis seedlings (A), and final root weight (B) and length (C) in switchgrass. Graphed data represent mean ± SD of five biological replicates

Fig. 2

Phylogenetic tree of Sphingobium sp. strain AEW4 and closely related Sphingobium species. Sphingomonas ginsensoli was used as an outgroup. The maximum-likelihood tree was constructed using the MEGAX software with an alignment of 1494 nucleotides and bootstrapping (n = 1000)

Fig. 3

Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) of Sphingobium species. Heat maps show the variation in A) Average Nucleotide Identity (ANI) and B) Average Amino Acid Identity (AAI) for Sphingobium sp. strain AEW4 and 17 different species in the genus Sphingobium. The values scale shows percent similarity based on nucleotides, with red representing a low identity and green representing a high identity

Fig. 4

Genome-wide comparison of orthologous clusters between strain AEW4 and its two closest relatives. Proportions of shared and unique clusters in comparisons with Sphingobium xenophagum and Sphingobium hydrophobicum are shown in the Venn diagram, based on OrthoVenn analysis. Strain AEW4 contains 80 unique clusters when compared to these two species, with 208 proteins which are classified in the pie chart based on their functional role

Fig. 5

Comparison of key functional gene categories in Sphingobium sp. strain AEW4 with the other members of the genus Sphingobium. Numbers of genes are shown for monosaccharide metabolism (A), osmotic stress (B), and fermentation (C) for Sphingobium sp. strain AEW4, its two closest relatives, S. xenophagum and S. hydrophobicum, and other genomes within the genus, including an average ± SD for these nine members

Fig. 6

Organization of the fructose operon present in Sphingobium sp. strain AEW4. Unique genes identified in the genome of strain AEW4 are shown and compared to closest gene matches in operons of Novosphingobium mathurense and Novosphingobium pentaromativorans US6-1

Fig. 7

Fructose growth dynamics of Sphingobium species. Growth of Sphingobium sp. AEW4 and Sphingobium xenophagum on fructose as the sole carbon source. Growth dynamics data represent the mean ± SD between three biological replicates