Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants with great carcinogenic threaten, and metal/PAH-contaminated environments represent one of the most difficult remedial challenges. In this work, Sphingobium yanoikuyae SJTF8 was isolated and identified with great and stable PAH-degrading efficiency even under stress conditions. It could utilize typical PAHs (naphthalene, phenanthrene, and anthracene) and heterocyclic and halogenated aromatic compounds (dibenzothiophene and 9-bromophenanthrene) as the sole carbon source. It could degrade over 98% of 500 mg/L phenanthrene in 4 days, and the cis-3,4-dihydrophenanthrene-3,4-diol was the first-step intermediate. Notably, strain SJTF8 showed great tolerance to heavy metals and acidic pH. Supplements of 0.30 mM of Cu2+, 1.15 mM of Zn2+, and 0.01 mM of Cd2+ had little effect on its cell growth and phenanthrene degradation; phenanthrene of 250 mg/L could still be degraded completely in 48 h. Further, the whole genome sequence of S. yanoikuyae SJTF8 was obtained, and three plasmids were found. The potential genes participating in stress-tolerance and PAH-degradation were annotated and were found mostly distributed in plasmids 1 and 2. Elimination of plasmid 2 resulted in the loss of the PAH-degradation ability. On the basis of genome mining results, the possible degrading pathway and the metabolites of S. yanoikuyae SJTF8 to phenanthrene were predicted.

Genome Sequence and Characterisation of Peribacillus sp. Strain AS_2, a Bacterial Endophyte Isolated from Alectra sessiliflora

“…Several genes involved in heavy metal resistance were identified in the genome of strain AS_2, such as genes responsible for copper resistance, the CopC/CopD family protein, the heavy metal translocating Ptype ATPase, and a magnesium transporter. In a similar study by [102], the bacterium Sphingobium yanoikuye strain SJTF8 was shown to be resistant to heavy metals such as copper, cadmium, and zinc and further showed degrading capabilities when co-cultured with these heavy metals with polycyclic aromatic hydrocarbons (PAHs), which are a group of hydrophobic compounds known for their toxic, carcinogenic, and mutagenic effects [103]. Other key enzymes required for initiating the degradation-like process, such as dioxygenases, have also been identified in the genome of AS_2, expanding the potential of this strain for bioremediation processes.…”

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

“…The enzymes involved in the conversion of NAP to salicylate can degrade PHE to 1H2Na. 1H2Na is hydroxylated to 1,2-dihydroxynaphthalene, which then enters the NAP-degradation pathway ( Yin et al, 2020 ). In Pseudomonas sp.…”

Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source

“…The degradation experiment was performed in triplicate by measuring the residual PHE concentration in the total culture volume [23,24]. Due to PHE's very low solubility, traditional methods were inadequate.…”