Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium

Abstract

Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills

“…However, there are no previous reports on its utilization of AKD, resin acids and cellulose. The discoloration of dyes by Klebsiella pneumoniae ( Zablocka-Godlewska et al, 2015 ; Abdulsalam et al, 2020 ) and the utilization of polycyclic aromatic hydrocarbons by Sphingomonas paucimobilis ( Lu et al, 2019 ; Ravintheran et al, 2019 ) are consistent with our results for Klebsiella sp. strain Y14A-BTP and Sphingomonas sp.…”

A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

“…Memebers of Verrucomicrobia colonized in intercellular spaces and inside root cells of rice, and produced IAA and its precursors IAM (indole-acetamide) or IPA (indole-3-pyruvic acid) for the plant growth promotion, showed activity of acid phosphatases for the solubilization of organic phosphates, and possessed also genes for citrate synthase [ 45 ]. Members of the Sphingomonas and Variovorax genera can survive in low nutrient environment, often be isolated from oil-contaminated soil due to their unique wide range of xenobiotic-biodegradative abilities [ 54 , 55 ]. Streptomyces bacteria, famous for producing secondary metabolites including antibiotics, may be used as plant probiotics due to the beneficial effects on plants and are not only ubiquitous in soil, but also are isolated from plant roots [ 56 ].…”

A few dominant bacteria and their genomic basis in mediating distinct ecosystem functions

“…4D and S7), which agrees with the top two taxa of Sphingomonas and Arthrobacter genera (collectively accounting for ~52.50% of total abundance, Fig. S6B) known to have a wide range of xenobiotic‐biodegradative abilities (Vandera et al ., 2015; Ravintheran et al ., 2019). These xenobiotic‐related genes potentially enhance the adaptation of these specialists to habitats containing toxic compounds. Fast growth strategy: Between the EF generalists and specialists, we found a non‐significant difference in the number of 16S rRNA genes, an estimate for rRNA operon copy number (Fig.…”

“…[Color figure can be viewed at wileyonlinelibrary.com] Fig. S6B) known to have a wide range of xenobioticbiodegradative abilities (Vandera et al, 2015;Ravintheran et al, 2019). These xenobiotic-related genes potentially enhance the adaptation of these specialists to habitats containing toxic compounds.…”