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.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

“…Nevertheless, the significant enrichment of this species in the Control and treated AMD water-irrigated soils (Group 2) than Group 1 indicate its low tolerance to acidic pH and HM toxicity. Anecdotal evidence suggests that the genus Sphingobium contains a small number of plant-growth promoting rhizobacteria (PGPR), with most taxa in this genus playing an important role in biodegradation and bioremediation in sediments and sandy soils [ 61 ]. This provides a clue of their potential involvement in maintaining and/or improving soil health in Group 2 samples.…”

Diversity and functional assessment of indigenous culturable bacteria inhabiting fine-flavor cacao rhizosphere: Uncovering antagonistic potential against Moniliophthora roreri

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Sphingobium cyanobacteriorum sp. nov., isolated from fresh water

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