Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0–100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30–100 cm to 0–30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs.

Co-inoculation of antagonistic Bacillus velezensis FH-1 and Brevundimonas diminuta NYM3 promotes rice growth by regulating the structure and nitrification function of rhizosphere microbiome

“…Some studies have also found that inoculation with Bacillus can stimulate the growth of Pseudomonas ( Qin et al, 2017 ; Wan et al, 2018 ; Sun et al, 2021 ). Although some Sphingomonas species have been reported to promote plant growth under stress conditions, the more prominent function of Sphingomonas is to remediate environmental contamination ( Asaf et al, 2020 ; Zhou et al, 2022 ). Lysobacter possesses many lytic enzymes and plays a key role in the degradation of complex macromolecules and plant pathogens present in soil ( Brescia et al, 2020 ; Moon et al, 2021 ).…”

Global Meta-Analysis of Urine Microbiome: Colonization of PAH-degrading bacteria among bladder cancer patients

“…It is interesting to point out that Sphingomonas, Acinetobacter and Micrococcus are some of few genera with the ability to breakdown polycyclic aromatic hydrocarbons (PAHs), a known BCa carcinogen. Having the ability to breakdown PAHs within urine, provides Sphingomonas and Acinetobacter a competitive advantage and ability to maintain dominance [41]. Furthermore, the organisms which were found to be overly abundant in BCa urine across all cohorts include Enterobacter, and Ralstonia, all also known PAHs metabolizers [42].…”

Draft Genome Sequence of Endophytic Sphingomonas faeni Strain ALB2, Isolated from the Leaf of a Cold-Desert Medicinal Plant

“…Characterized by the presence of glycosphingolipids in their outer membranes, Sphingomonas strains are integral components of soil and plant microbiomes ( 1 , 2 ). Many species of Sphingomonas display plant-beneficial activities ( 3 , 4 ) and confer bioremediation in soil ( 5 ). During ongoing work on microbial endophytes, we identified a bacterial strain, ALB2, with closest similarity to Sphingomonas faeni strain MA-olki (GenBank accession number AJ429239 ) on the basis of 16S rRNA gene sequence analysis using the EzTaxon database.…”