PLoS One
·
2018
·Vol. 13
·期 10
·e0204324
·
IF 2.766
Fangfang Li,Yidan Liu,Diwei Wang,Chaosheng Zhang,Zhihui Yang,Siqi Lu,Yangyang Wang
A halotolerant bacterial consortium capable of degrading di-(2-ethylhexyl) phthalate (DEHP) was enriched from activated sludge. Community analysis revealed that LF contained seven families and seven genera of bacteria. The predominant species was Gordonia sp. (54.93%), Rhodococcus . sp. (9.92%) and Achromobacter sp. (8.47%). The consortium could degrade 93.84% of 1000 mg/l DEHP after 48 h incubation. The optimal temperature and pH for LF to degrade DEHP were 30 °C and 6.0, respectively. LF degraded more than 91% of DEHP with salt concentrations ranging from 0–3%. The inoculum size had great effects on DEHP degradation (incubation time < 24h). LF could degrade high concentrations of DEHP (from 100 to 2000 mg/l) with the degradation ratio above 92% after 72 h incubation. Kinetics analysis revealed that the degradation of DEHP by LF was best fitted by the first-order kinetics when the initial concentration ranged from 100 to 2000 mg/l. The main intermediates (2-ethylhexyl pentyl phthalate, butyl (2-ethylhexyl) phthalate (BEHP), mono-ethylhexyl phthalate (MEHP), mono-hexyl phthalate (MHP), mono-butyl phthalate (MBP)) in DEHP degradation process were identified using gas chromatography–mass spectrometry (GC-MS), and a new complex biochemical pathway was proposed. Furthermore, LF could also degrade dimethyl phthalate (DMP), diethyl phthalate (DEP), di- n -butyl phthalate (DBP), di- n -octyl phthalate (DOP) and phthalic acid (PA).
研究领域:
环境科学
·
微生物学
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高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2026
·
IF 4.2
Nan Meng,Genxiu Li,Jiaxin Zhang,Jingwen Zhu,Xutong Kang,Jiahao Duan,Qiao Ma
Skatole (3-methylindole), a persistent and toxic N-heterocyclic aromatic pollutant, poses significant bioremediation challenges due to poorly defined biodegradation processes. This study systematically investigated the genetic determinants and metabolic mechanisms of skatole degradation in the environmentally versatile Gram-positive genus Rhodococcus. We demonstrated that skatole degradation was a broadly conserved trait across diverse Rhodococcus species, including R. aetherivorans, R. pyridinivorans, R. ruber, and R. qingshengii. Genomic and functional analyses uncovered a novel flavoprotein monooxygenase (FPMO) SkaA as the initial catalyst for skatole catabolism. Heterologous expression in Escherichia coli confirmed SkaA’s essential catalytic role, with high-resolution liquid chromatography-tandem mass spectrometry identifying the key products 3-methyloxindole and 3-hydroxy-3-methyloxindole. Distribution studies revealed SkaA homologs predominantly in Actinobacteria, particularly Nocardia and Rhodococcus, indicating metabolic capacity for skatole transformation within this phylum. Notably, Rhodococcus strains lacking the skaA gene also retained skatole degradation activity, implying the existence of alternative genetic determinants. Crucially, phylogenetic analysis positioned SkaA as a distinct subclass within Group E FPMOs, exhibiting ≤40% sequence identity to reported styrene/indole oxygenases. The phylogenetic segregation of skatole, indole, and styrene monooxygenases provides a predictive framework for functional annotation of Group E FPMOs. Our findings elucidate a novel skatole transformation pathway, establish Rhodococcus as environmentally versatile biocatalysts, and provide new insights into the study of Group E FPMOs.
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CHEMOSPHERE
·
2023
·
IF 8.8
Xiaoyuan Guo,Lan Qiu,Zhiwei Liang,Qihong Lu,Shanquan Wang,Hojae Shim
The coronavirus disease 2019 (COVID-19) pandemic has significantly increased the demand of disinfectant use. Chloroxylenol ( para -chloro- meta -xylenol, PCMX) as the major antimicrobial ingredient of disinfectant has been widely detected in water environments, with identified toxicity and potential risk. The assessment of PCMX in domestic wastewater of Macau Special Administrative Region (SAR) showed a positive correlation between PCMX concentration and population density. An indigenous PCMX degrader, identified as Rhodococcus sp. GG1, was isolated and found capable of completely degrading PCMX (50 mg L −1 ) within 36 h. The growth kinetics followed Haldane's inhibition model, with maximum specific growth rate, half-saturation constant, and inhibition constant of 0.38 h −1 , 7.64 mg L −1 , and 68.08 mg L −1 , respectively. The degradation performance was enhanced by optimizing culture conditions, while the presence of additional carbon source stimulated strain GG1 to alleviate inhibition from high concentrations of PCMX. In addition, strain GG1 showed good environmental adaptability, degrading PCMX efficiently in different environmental aqueous matrices. A potential degradation pathway was identified, with 2,6-dimethylhydroquinone as a major intermediate metabolite. Cytochrome P450 (CYP450) was found to play a key role in dechlorinating PCMX via hydroxylation and also catalyzed the hydroxylated dechlorination of other halo-phenolic contaminants through co-metabolism. This study characterizes an aerobic bacterial pure culture capable of degrading PCMX metabolically, which could be promising in effective bioremediation of PCMX-contaminated sites and in treatment of PCMX-containing waste streams.
研究领域:
环境科学
·
微生物学
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PubMed
高影响因子
RSC Advances
·
2026
·Vol. 16
·期 9
·8166-8177
·
IF 6.1
Yifei Meng,Xuan Ou,Zhenghui Liu,Shun Yao,Chuxiao Hu,Qiuchi Yu,Wenjie Xia
Achieving sustainable and cost-effective production and modulating the structure of biosurfactants is increasingly obtaining attention due to carbon neutrality and eco-safety. Nanotechnology-assisted approaches have been emerging as a promising strategy for this purpose. Here, we investigated the effect of metal oxide nanoparticles on the yield and molecular structure of trehalose lipids produced by Rhodococcus erythropolis WJ-2. Sunflower oil was identified as the optimal carbon source against other oils, yielding 12.60 g L−1. Subsequent optimization of four key medium components (sunflower oil, ZnSO4, (NH4)2SO4, and yeast extract) using a Box–Behnken design elevated the baseline yield to 24.75 g L−1. Interestingly, the trehalose lipid yield was further enhanced to 28.12 g L−1 compared to the optimized medium without NPs when supplemented with 0.5 g per L Fe2O3 NPs (≈20 nm). Furthermore, structural diversity analyzed by FTIR and HPLC-MS showed the obvious m/z value shifts of trehalose lipids with NPs comprising longer hydrophobic fatty acid chains and more unsaturated fatty acid derivatives. In the absence of Fe2O3 NPs, the main m/z peaks were detected at m/z 496, 694, 877, and 1044 (relative abundances: 14.19%, 27.08%, 44.18%, 14.55%), corresponding to short-to-medium-chain fatty acid derivatives (e.g., methyl hexanoate, methyl octanoate). In contrast, the dominant peaks shifted to m/z 673, 807, 874, and 1043 (relative abundances: 22.21%, 18.39%, 47.64%, 11.76%) with Fe2O3 NP supplementation. These findings suggest that the unique redox properties and high surface area of Fe2O3 nanoparticles could enhance the yield and modulate the structures to enable the tailored biosynthesis of glycolipids by influencing key-enzyme activity and metabolic flux. This nanoparticle-assisted fermentation strategy offers a promising route for the scalable production of designer biosurfactants for diverse industrial applications.
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高影响因子
Microbial Cell Factories
·
2026
·
IF 4.9
Ma Jinglin,Zhuang Yan,Guan Huiting,Zhang Zhenjun,Zhu Ning,Han Changze,Wang Yonggang,Chen Jixiang
Cytochrome P450 monooxygenases (CYPs) constitute a versatile family of biocatalysts capable of regio- and stereoselective hydroxylation, offering significant potential for pharmaceutical synthesis and the environmental remediation of endocrine-disrupting steroids. Although their synthetic utility is widely recognized, the mechanistic basis of their activity, particularly in bacteria, remains insufficiently explored. Building on prior discovery of steroid-degrading activity in Rhodococcus erythropolis KB1, in this study, we functionally characterized three putative P450 enzymes (CYP125ARh1, CYP125ARh2, and CYP153ARh3) identified from its genome. Substrate-binding assays demonstrated strong affinity toward progesterone and testosterone, but negligible affinity for 11β-hydroxysteroids, including cortisol and corticosterone. In vitro conversion assays revealed that all three enzymes specifically catalyze 16α-hydroxylation of progesterone and testosterone, although with varying catalytic efficiencies. Among them, CYP125ARh2 was identified as the most efficient enzyme, achieving near-quantitative conversion of progesterone (88%) and testosterone (62%). Kinetic analysis further underscored the superior catalytic properties of CYP125ARh2, which displayed lower Michaelis constants (K m = 16.41 ± 1.97 µM for progesterone and 24.50 ± 2.60 µM for testosterone) and higher turnover rates (V max = 6.05 ± 0.16 µM/min and 5.09 ± 0.13 µM/min, respectively). The superior catalytic efficiency of CYP125ARh2 originates from its unique active site architecture, which integrates a pre‑organized, synergistic residue network with pronounced induced‑fit plasticity. This structural synergy enables precise substrate positioning and optimal reaction geometry, thereby rationalizing its high 16α‑hydroxylation activity toward both progesterone and testosterone. These findings highlight CYP125ARh2 as a promising template for engineering high-performance biocatalysts. Overall, this work provides foundational insights into the role of the P450 enzymes in steroid chemistry and the biodegradation of steroidal pollutants.
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高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2026
·
IF 4.2
Zhengyu Hou,Hejuan Pan,Shihan Wang,Yulin Li,Yang Yu,Pei Qiao,Haixia Wang,Weihong Zhong
Phthalate esters (PAEs) are ubiquitous in the environment, and their microbial metabolism is associated with transport proteins. In this study, multiple novel membrane proteins were identified, revealing their pivotal role in PAEs degradation. Based on whole-genome and transcriptomic analyses, approximately 20 potential PAEs transport membrane proteins were predicted to be involved in PAEs degradation by Rhodococcus sp. AH-ZY2. Among them, four protein genes (0620, 3572, 4497, and 5299) exhibited increased transcription levels (Log2F(c)>2.8) in response to di-n-octyl-phthalate (DnOP) as the sole carbon source, instead of fructose, were selected for functional verification. Gene knockout and complementation experiments showed that these four transport protein genes, belonging to the MFS family (0620, 3572, and 5299) and the ABC family (4497), respectively, exhibited the function to transport multiple PAEs into cells. Specifically, membrane protein 5299 could transport the most diverse kinds of PAEs. Molecular docking results also showed that Ser and Arg play a key role in the PAEs transport process of membrane protein 5299, and the PAEs-binding pocket size of 5299 in the transition region was larger than that of 0620, 3572, and 4497. Then, the expression of the genes encoding 0620, 3572, 5299, and 4497 was enhanced after they were cloned into the plasmid pNV18 and transformed into the strain AH-ZY2. The enhancement of 5299 expression exhibited a better improvement in PAEs degradation than the other three genes. This study provides four novel transport proteins and a new strategy for effective bioremediation of PAEs via enhanced membrane transport.
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高影响因子
BIODEGRADATION
·
2017
·Vol. 29
·期 1
·1-10
·
IF 2.018
Wang Hui,Hu Jinxing,Xu Kai,Tang Xianjin,Xu Xinhua,Shen Chaofeng
Two biphenyl-degrading bacterial strains, SS1 and SS2, were isolated from polychlorinated biphenyl (PCB)-contaminated soil. They were identified as Rhodococcus ruber and Rhodococcus pyridinivorans based on the 16S rRNA gene sequence, as well as morphological, physiological and biochemical characteristics. SS1 and SS2 exhibited tolerance to 2000 and 3000 mg/L of biphenyl. And they could degrade 83.2 and 71.5% of 1300 mg/L biphenyl within 84 h, respectively. In the case of low-chlorinated PCB congeners, benzoate and 3-chlorobenzoate, the degradation activities of SS1 and SS2 were also significant. In addition, these two strains exhibited chemotactic response toward TCA-cycle intermediates, benzoate, biphenyl and 2-chlorobenzoate. This study indicated that, like the flagellated bacteria, non-flagellated Rhodococcus spp. might actively seek substrates through the process of chemotaxis once the substrates are depleted in their surroundings. Together, these data provide supporting evidence that SS1 and SS2 might be good candidates for restoring biphenyl/PCB-polluted environments.
研究领域:
环境微生物学
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生物修复
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微生物生态学
·
趋化性
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高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2025
·
IF 3.7
Yan Zhang,Huan Liu,Shan Yu,Ruocheng Pei,Haiyang Hu,Weiwei Wang,Ping Xu,Hongzhi Tang
Oil contamination poses significant risks to human health and ecosystems, emphasizing the importance of studying alkane biodegradation. In this study, we found that Rhodococcus erythropolis XP can utilize various alkanes, including C16–C36 n-alkanes and iso-alkane (pristane). The degradation capacity was significant, with over 95% of C20 degraded (500–2,500 mg/L) within 72 h. The bioremediation capacity in oily sludge was determined by a novel Low Pressure Gas Chromatography-Mass Spectrometry methodology especially for rapid analysis (within 12 min) of n-alkanes. Notable biodegradation of C14–C30 alkanes was observed in sludge treated with Rhodococcus erythropolis XP. In addition, metabolic intermediates of C16 and C20 were identified, indicating the presence of both terminal and subterminal pathways in Rhodococcus erythropolis XP. A new Baeyer-Villiger monooxygenase (BVMO_4041) was characterized, which catalyzes a key step in the subterminal pathway of alkane degradation. These results reflect the promise of Rhodococcus erythropolis XP in addressing the pressing need for efficient alkane degradation in contaminated environments.
研究领域:
环境微生物学
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生物修复
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石油烃降解
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应用微生物学
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分析化学
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高影响因子
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2024
·Vol. 31
·期 14
·21659-21667
·
IF 0
Pan Hanqing,Ma Qiao,Zhang Jiaxin,Hu Haodong,Dai Huiyu,Shi Yuyan,Lu Shuxian,Wang Jingwei
Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater treatment plants, rivers, seawater, and even drinking water, with concentrations ranging from ng/L to mg/L. However, the biodegradation of chloroxylenol received limited attention with only sporadic reports available so far. In this study, an efficient chloroxylenol-degrading consortium, which could degrade 20 mg/L chloroxylenol within two days, was obtained after five months of enrichment. Amplicon sequencing analysis revealed a decrease in the α-diversity (e.g., Shannon index and Inv_Simpson index) of the community during the domestication process. Microbial community dynamics were uncovered, with sequences affiliated to Achromobacter , Pseudomonas , and Rhodococcus identified as the most abundant taxonomic groups. From the consortium, five pure isolates were obtained; however, it was found that only one strain of Rhodococcus could degrade chloroxylenol. Strain Rhodococcus sp. DMU2021 could degrade chloroxylenol efficiently under the conditions of temperature 30–40 °C, and neutral/alkaline conditions. Chloroxylenol was toxic to strain DMU2021 and triggered both enzymatic and non-enzymatic antioxidant systems in response. This study provides novel insights into the biodegradation process of chloroxylenol, as well as valuable bioresources for bioremediation.
研究领域:
环境科学
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微生物学
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生物技术
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生态毒理学
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BIORESOURCE TECHNOLOGY
·
2015
·
IF 4.494
Shumei Fang,Xuejiao An,Hongyuan Liu,Yi Cheng,Ning Hou,Lu Feng,Xinning Huang,Chunyan Li
Nitriles are common environmental pollutants, and their removal has attracted increasing attention. Microbial degradation is considered to be the most acceptable method for removal. In this work, we investigated the biodegradation of three aliphatic nitriles (acetonitrile, acrylonitrile and crotononitrile) by Rhodococcus rhodochrous BX2 and the expression of their corresponding metabolic enzymes. This organism can utilize all three aliphatic nitriles as sole carbon and nitrogen sources, resulting in the complete degradation of these compounds. The degradation kinetics were described using a first-order model. The degradation efficiency was ranked according to t 1/2 as follows: acetonitrile > trans-crotononitrile > acrylonitrile > cis-crotononitrile. Only ammonia accumulated following the three nitriles degradation, while amides and carboxylic acids were transient and disappeared by the end of the assay. mRNA expression and enzyme activity indicated that the tested aliphatic nitriles were degraded via both the inducible NHase/amidase and the constitutive nitrilase pathways, with the former most likely preferred.
研究领域:
环境微生物学
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生物修复
·
酶学
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PubMed
高影响因子
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
·
2026
·
IF 3.4
Jinglin Ma,Yan Zhuang,Huiting Guan,Zhenjun Zhang,Ning Zhu,Changze Han,Yonggang Wang,Jixiang Chen
The release and prolonged retention of steroid hormones pose significant risks to both human health and the environment. Research on efficient-degrading bacteria at higher concentrations and their degradation pathways, genes, and enzymes is limited. In this study, Rhodococcus erythropolis KB1 efficiently degraded 96.75% of 50 mg/L 17β-estradiol (E2) within nine days. Including the 4,5- and 9,10-seco pathways, five putative degradation pathways were identified based on the analysis of metabolic intermediates and products using high-performance liquid chromatography–quadrupole–time-of-flight–mass spectrometry (HPLC-Q-TOF-MS). Under the proposed aerobic pathways, E2 undergoes hydroxylation or cleavage at ring A or B. The resultant products are subsequently converted into a common steroid metabolite, 3aα-H-4α(3′-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), via β-oxidation. HIP is further degraded through a central pathway and ultimately assimilated into the tricarboxylic acid (TCA) cycle. Whole-genome sequencing predicted a steroid degradation-related gene cluster on contig NZ_CP050127.1 . Transcriptomic analysis demonstrated that the expression of the short-chain dehydrogenase (SDR) gene and three cyp genes in this gene cluster were significantly induced by E2. Additionally, the global response of E2 in strain KB1 was analyzed using transcriptome analysis. Various genes involved ATP-binding cassette (ABC) transport system, electron transfer and energetic metabolism, and stress response—were significantly increased in mRNA levels in response to strain KB1 that can use E2 as the single carbon source. These findings highlight strain KB1 as a promising candidate for E2 biodegradation, offer novel insights into the microbial mechanisms of E2 catabolism, and establish a theoretical basis for future applications.
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高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2024
·
IF 12.2
Zhengyu Hou,Hejuan Pan,Mengjie Gu,Xiaowang Chen,Tongtong Ying,Pei Qiao,Junwei Cao,Haixia Wang,Tong Hu,Lianbao Zheng,Weihong Zhong
Phthalate esters (PAEs) are widely used as plasticizers and cause serious complex pollution problem in environment. Thus, strains with efficient ability to simultaneously degrade various PAEs are required. In this study, a newly isolated strain Rhodococcus sp. AH-ZY2 can degrade 500 mg/L Di-n-octyl phthalate completely within 16 h and other 500 mg/L PAEs almost completely within 48 h at 37 °C, 180 rpm, and 2 % (v/v) inoculum size of cultures with a OD 600 of 0.8. OD 600 = 0.8, 2 % (v/v). Twenty genes in its genome were annotated as potential esterase and four of them ( 3963 , 4547 , 5294 and 5359 ) were heterogeneously expressed and characterized. Esterase 3963 and 4547 is a type I PAEs esterase that hydrolyzes PAEs to phthalate monoesters. Esterase 5294 is a type II PAEs esterase that hydrolyzes phthalate monoesters to phthalate acid (PA). Esterase 5359 is a type III PAEs esterase that simultaneously degrades various PAEs to PA. Molecular docking results of 5359 suggested that the size and indiscriminate binding feature of spacious substrate binding pocket may contribute to its substrate versatility. AH-ZY2 is a potential strain for efficient remediation of PAEs complex pollution in environment. It is first to report an esterase that can efficiently degrade mixed various PAEs.
研究领域:
微生物学
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环境科学
·
生物化学
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PubMed
高影响因子
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