Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis

Zhai, Ying; Ma, Jiajun; Gao, Guohui; Cui, Yumeng; Ying, Ming; Zhao, Yihe; Antunes, Agostinho; Huang, Lei; Li, Meitong

doi:10.3390/microorganisms13112608

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Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis

by

Ying Zhai

¹,

Jiajun Ma

¹,

Guohui Gao

¹,

Yumeng Cui

¹,

Ming Ying

¹,

Yihe Zhao

^2,3

,

Agostinho Antunes

^2,3

,

Lei Huang

^1,*

and

Meitong Li

^1,*

¹

Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China

²

CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal

³

Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal

^*

Authors to whom correspondence should be addressed.

Microorganisms 2025, 13(11), 2608; https://doi.org/10.3390/microorganisms13112608 (registering DOI)

Submission received: 22 September 2025 / Revised: 10 November 2025 / Accepted: 14 November 2025 / Published: 16 November 2025

(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)

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Abstract

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.

Keywords: phenanthrene; rhamnolipid; biodegradation; cell surface characterisation; transcriptome analysis

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MDPI and ACS Style

Zhai, Y.; Ma, J.; Gao, G.; Cui, Y.; Ying, M.; Zhao, Y.; Antunes, A.; Huang, L.; Li, M. Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis. Microorganisms 2025, 13, 2608. https://doi.org/10.3390/microorganisms13112608

AMA Style

Zhai Y, Ma J, Gao G, Cui Y, Ying M, Zhao Y, Antunes A, Huang L, Li M. Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis. Microorganisms. 2025; 13(11):2608. https://doi.org/10.3390/microorganisms13112608

Chicago/Turabian Style

Zhai, Ying, Jiajun Ma, Guohui Gao, Yumeng Cui, Ming Ying, Yihe Zhao, Agostinho Antunes, Lei Huang, and Meitong Li. 2025. "Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis" Microorganisms 13, no. 11: 2608. https://doi.org/10.3390/microorganisms13112608

APA Style

Zhai, Y., Ma, J., Gao, G., Cui, Y., Ying, M., Zhao, Y., Antunes, A., Huang, L., & Li, M. (2025). Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis. Microorganisms, 13(11), 2608. https://doi.org/10.3390/microorganisms13112608

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Enhancing Phenanthrene Degradation by Burkholderia sp. FM-2 with Rhamnolipid: Mechanistic Insights from Cell Surface Properties and Transcriptomic Analysis

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