Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent organic pollutants composed of two or more fused benzene rings, posing serious threats to ecological environments and human health. Biodegradation is an efficient, economical, and sustainable approach for remediating PAHs pollution. In our previous work, we isolated and characterized a PAH-degrading bacterium, Burkholderia sp. FM-2. FM-2 demonstrated strong tolerance and efficient degradation capacity toward various PAHs, achieving 81.98% degradation of 2 mM phenanthrene within 3 days, and over 58% degradation of 2 mM fluorene, dibenzofuran, and dibenzothiophene under the same conditions. Through combined genomic and transcriptomic analyses, a putative PAH degradation gene cluster was identified in the FM-2 genome. Phylogenetic and domain architecture analyses were conducted on seven oxygenase genes within the cluster. Using AlphaFold 3, we predicted the three-dimensional structure of the downstream transport protein OmpW and proposed a potential transmembrane channel for PAHs uptake. To eliminate the phenanthrene degradation intermediate 1-hydroxy-2-naphthoic acid, a genetically engineered strain FM-2::nahG was constructed by heterologous expression of the salicylate hydroxylase gene (nahG). The modified strain completely abolished the accumulation of 1-hydroxy-2-naphthoic acid and achieved complete mineralization of phenanthrene. This study not only reveals the molecular basis of PAHs degradation in Burkholderia sp. FM-2 but also demonstrates the potential of metabolic engineering to enhance biodegradation ability, providing a promising microbial candidate for the bioremediation of PAH-polluted environments.

Various surfactants have been applied for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated environments, but their roles in bioremediation remain controversial. This study focused on rhamnolipid (a typical surfactant) and Burkholderia sp. FM-2 (a high-efficiency phenanthrene-degrading bacterium), investigating its effects on phenanthrene solubilization and biodegradation by analyzing cell surface characteristics and gene expression differences. Results showed that low concentrations of rhamnolipid (20–120 mg/L) promoted phenanthrene degradation, while high concentration (400 mg/L) exerted an inhibitory effect. At 20–56 mg/L, rhamnolipid altered the bacterial surface morphology and functional groups, facilitated lipopolysaccharide release, enhanced cell surface hydrophobicity, and increased zeta potential. When the rhamnolipid concentration was 20 mg/L, the phenanthrene degradation rates of cytoplasmic enzymes, periplasmic enzymes, and extracellular enzymes produced by the bacterium reached over 98% after 15 days of enzyme system culture, demonstrating its role in promoting enzyme production and activity. Transcriptomic analysis revealed that 56 mg/L (1 CMC) rhamnolipid enhanced degradation through multi-pathway regulation of gene expression: upregulating the gene encoding protocatechuate 3,4-dioxygenase to strengthen benzene ring cleavage; increasing the expression of genes related to ABC transporters and protein transport to promote phenanthrene transmembrane transport; and activating genes involved in metabolic processes such as pyruvate metabolism and the tricarboxylic acid (TCA) cycle to enhance central carbon metabolic flux. This regulatory mode optimizes energy supply and redox balance, and indirectly improves phenanthrene bioavailability by modulating membrane structure and function.

Co-contamination with dibenzofuran (DBF) and cadmium (Cd(II)) poses a major challenge in environmental remediation. While Burkholderia sp. can degrade polycyclic aromatic hydrocarbons and tolerate heavy metals, the coordinated mechanism governing DBF degradation under high Cd(II) stress remains elusive. Here, we characterize Burkholderia sp. FM-2, which optimally degrades 600 mg/L DBF at pH 6.0 and 25 °C, achieving 91.8% removal within 48 h. FM-2 exhibits exceptional Cd(II) tolerance, with a minimum inhibitory concentration of 2000 mg/L. UPLC-MS/MS confirms DBF degradation via dioxygenase-mediated hydroxylation and sequential enzymatic reactions. Transcriptomics reveals, for the first time, concurrent upregulation of genes encoding RND efflux pumps, ABC transporters, P-type ATPases, and core DBF-degrading enzymes under high Cd(II) stress, enabling the synergistic maintenance of intracellular Cd(II) homeostasis and efficient DBF degradation. Collectively, FM-2 remediates DBF-Cd(II) co-contamination via coordinated transcriptional regulation of degradation and detoxification pathways, offering a promising strain resource and molecular basis for the bioremediation of co-contaminated environments.

Co-contamination of biphenyl and heavy metals is widespread in industrial environments, but systematic studies on the simultaneous treatment of both pollutants using a single microbial strategy remain limited. In this study, we characterized the biphenyl degradation performance, metabolic pathway, transcriptomic response, and Cr(VI) tolerance of Rhodococcus sp. TG-1, and developed an alkali-modified biochar immobilization system to enhance its degradation efficiency for biphenyl under Cr(VI) stress. Degradation experiments were carried out under optimal conditions (30 °C, pH 7.0), and it was found that strain TG-1 degraded 76.84% of 300 mg/L biphenyl within 3 days. Intermediate metabolites were identified by LC-MS, and five key intermediates were detected, confirming that TG-1 metabolizes biphenyl via the classical 2,3-dihydroxybiphenyl dioxygenase pathway, with subsequent entry into the tricarboxylic acid cycle. Transcriptomic analysis was performed to profile gene expression, revealing 845 differentially expressed genes under biphenyl stress, including 672 upregulated genes significantly enriched in aromatic degradation pathways. Seven complete bph gene clusters responsible for biphenyl catabolism were also identified. Strain TG-1 exhibited high tolerance to Cr(VI), with a minimum inhibitory concentration (MIC) of 500 mg/L. However, its biphenyl degradation efficiency dropped to 51.32% in the presence of 200 mg/L Cr(VI). After immobilization using alkali-modified straw biochar (JBC), heavy metal toxicity was alleviated, and the biphenyl removal rate increased to 99.30% under co-contamination conditions. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) analyses confirmed that TG-1 was stably loaded onto the biochar surface through hydrogen bonding and electrostatic interactions. Altogether, this study provides a promising bacterial strain and a green immobilization strategy for enhancing biphenyl removal in the presence of Cr(VI), offering a practical approach for the treatment of environments co-contaminated with aromatic compounds and heavy metals.