Frontiers in Microbiology
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2023
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IF 5.2
Miao Lei,Chen Siyuan,Yang Hua,Hong Yaqi,Sun Liwen,Yang Jie,Sun Guanjun,Liu Yi,Li Chunyan,Zang Hailian,Cheng Yi
Triclocarban (TCC), an emerging organic contaminant (EOC), has become a severe threat to soil microbial communities and ecological security. Here, the TCC-degrading strain Rhodococcus rhodochrous BX2 and DCA-degrading strain Pseudomonas sp. LY-1 (together referred to as TC1) were immobilized on biochar to remove TCC and its intermediates in TCC-contaminated soil. High-throughput sequencing was used to investigate the microbial community structure in TCC-contaminated soil. Analysis of co-occurrence networks was used to explore the mutual relationships among soil microbiome members. The results showed that the immobilized TC1 significantly increased the removal efficiency of TCC from 84.7 to 92.7% compared to CK (no TC1 cells on biochar) in 10 mg/L TCC liquid medium. The utilization of immobilized TC1 also significantly accelerated the removal of TCC from contaminated soil. Microbial community analysis revealed the crucial microorganisms and their functional enzymes participating in TCC degradation in soil. Moreover, the internal labor division patterns and connections of TCC-degrading microbes, with a focus on strains BX2 and LY-1, were unraveled by co-occurrence networks analysis. This work provides a promising strategy to facilitate the bioremediation of TCC in soil, which has potential application value for sustainable biobased economies.
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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PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2019
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IF 5.589
Shanshan Sun,Haizhen Wang,Binxin Fu,Hao Zhang,Jun Lou,Laosheng Wu,Jianming Xu
Rhodococcus sp. WB9, a strain isolated from polycyclic aromatic hydrocarbons contaminated soil, degraded phenanthrene (PHE, 100 mg L −1 ) completely within 4 days. 18 metabolites were identified during PHE degradation, including 5 different hydroxyphenanthrene compounds resulted from multiple routes of initial monooxygenase attack. Initial dioxygenation dominantly occurred on 3,4-C positions, followed by meta -cleavage to form 1-hydroxy-2-naphthoic acid (1H2N). More than 95.2% of 1H2N was transported to and kept in extracellular solution without further degradation. However, intracellular 1H2N was converted to 1,2-naphthalenediol that was branched to produce salicylate and phthalate. Furthermore, 131 genes in strain WB9 genome were related to aromatic hydrocarbons catabolism, including the gene coding for salicylate 1-monooxygenase that catalyzed the oxidation of 1H2N to 1,2-naphthalenediol, and complete gene sets for the transformation of salicylate and phthalate toward tricarboxylic acid (TCA) cycle. Metabolic and genomic analyses reveal that strain WB9 has the ability to metabolize intracellular 1H2N to TCA cycle intermediates, but the extracellular 1H2N can’t enter the cells, restricting 1H2N bioavailability and PHE mineralization.
研究领域:
环境微生物学
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生物降解
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代谢组学
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基因组学
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PubMed
高影响因子
CHEMOSPHERE
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2022
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IF 8.943
Bohan Yuan,Jiachao Yao,Zeyu Wang,Luyao Dai,Min Zhao,Dzmitry Hrynsphan,Savitskaya Tatsiana,Jun Chen
In this work, Rhodococcus ruber HJM-8 and Paracoccus communis YBH-X were isolated and used to enhance N , N -dimethylacetamide (DMAC) degradation and mineralization efficiencies. The monoculture and co-culture of the two strains for DMAC degradation were compared; results indicated that, a degradation efficiency of 97.62% was obtained in co-culture, which was much higher than that of monocultures of HJM-8 (57.34%) and YBH-X (34.02%). The degradation mechanism showed that co-culture could efficiently improve extracellular polymeric substances production, electron transfer , and microbial activity . Meanwhile, the mineralization mechanism suggested that acetate was the dominant intermediate which had an inhibitory effect on HJM-8, and co-culture was conducive to mineralization due to the high performance of acetate conversion and Na + K + -ATPase vitality. Besides, a pathway of DMAC biodegradation was proposed for co-culture: DMAC was degraded into acetate by HJM-8, then the accumulated acetate was mineralized by YBH-X. Additionally, the co-culture system was further optimized by Box-Behnken design.
研究领域:
环境微生物学
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生物修复
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化学工程
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PubMed
高影响因子
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
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2022
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IF 7.129
Xiaolei Wang,Hong Lu,Qiansheng Li,Yang Zhou,Jiti Zhou
Anthraquinone compounds (ACs) could be efficiently degraded and detoxified by bacteria. However, the molecular mechanism of bacterial degradation and detoxification of ACs remains unclear. In this study, 1-aminoanthraquinone-2-sulfonate (ASA-2) was used as a model anthraquinone compound, the response mechanism of Rhodococcus pyridinivorans GF3 to ASA-2 using genomics and transcriptomics techniques was investigated. Comparative genome analysis showed that strain GF3 owned an especial gene region (Genes 1337–1399) containing the genes encoding cytochrome P450, monooxygenase, dehydrogenase and oxidoreductase, which did not commonly exist in Rhodococcus genus. The amino acid sequences of these genes were similar to those of the cleavage enzymes of anthraquinone ring in Aspergillus genus. Moreover, the transcriptions of Genes 1392–1394 (cytochrome 450 gene cluster) displayed 1.8–3.1-fold up-regulation under ASA-2 exposure. Meanwhile, as an intermediate product of ASA-2, catechol was degraded to acetyl-CoA, succinyl-CoA and pyruvate, resulting in the enhanced tricarboxylic acid cycle and ATP generation. This process also promoted the up-regulation of the genes encoding resistance, efflux, transporter and anti-oxidation pressure proteins, which were involved in resisting ASA-2 and maintaining the homeostasis of cells. These results provided us with a further understanding of the molecular mechanism of degradation and detoxification of ACs.
研究领域:
微生物学
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环境科学
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分子生物学
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基因组学
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转录组学
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PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
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2018
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IF 4.61
Hai-Ming Zhao,Rui-Wen Hu,Xue-Xue Chen,Xue-Bin Chen,Huixiong Lü,Yan-Wen Li,Hui Li,Ce-Hui Mo,Quan-Ying Cai,Ming-Hung Wong
A novel bacterial strain designated as Rhodococcus pyridinivorans XB, capable of utilizing various endocrine disruptor phthalates or phthalic acid (PA) as sole source of carbon and energy, was isolated from activated sludge. Under the optimal culture conditions (pH 7.08, 30.4 °C, inoculum size (OD 600 nm ) of 0.6) obtained by response surface methodology, di-(2-ethylhexyl) phthalate (DEHP, 200 mg/L) could be degraded by strain XB with a removal rate of 98% within 48 h. Under the observation of an atomic force microscope, it was confirmed that DEHP did not inhibit the growth of strain XB which might produce some extracellular polymeric substances as a response to DEHP stress, resulting in rapid degradation of DEHP. At initial concentrations of 50–800 mg/L DEHP, its degradation curves were well fitted with the first-order kinetic model, and the half-life of DEHP degradation varied from 5.44 to 23.5 h. The degradation intermediates of DEHP were identified by both GC–MS and high performance liquid chromatography–time of flight-mass spectrometry (HPLC–TOF-MS). Significant up-regulation was observed for the relative expression levels of genes (i.e., phthalate hydrolase, PA 3,4-dioxygenase, protocatechuate 3,4-α and 3,4-β dioxygenase) involved in DEHP degradation determined by real-time quantitative PCR (RT-qPCR). A DEHP biodegradation pathway by strain XB was proposed based on the identified intermediates and the degrading genes. Bioaugmentation of DEHP-contaminated soils with strain XB could efficiently promote DEHP removal, offering great potential in bioremediation of DEHP-contaminated environment.
研究领域:
环境微生物学
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生物修复
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分子生物学
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环境工程
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PubMed
高影响因子
Frontiers in Microbiology
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2024
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IF 4
Qiannan Li,Hanyu Pan,Peng Hao,Zhenhua Ma,Xiaojun Liang,Lianyu Yang,Yunhang Gao
The 17β-estradiol (E2)-degrading bacterium Rhodococcus sp.RCBS9 previously showed remarkable resistance to the combined stresses of low temperature and E2. In this study, physiological experiments and transcriptomic analysis were performed to investigate the mechanisms underlying the strain's low-temperature adaptation and briefly analyze how it maintains its ability to degrade E2 at low temperature. The results showed that the strain's signal transduction functions, adaptive changes in cell membrane and cell wall structure, gene repair functions, and synthesis of antioxidants and compatible solutes are key to its ability to adapt to low temperature. In addition, its stress proteins in response to low temperature were not typical cold shock proteins, but rather universal stress proteins (USPs) and heat shock proteins (HSPs), among others. The strain also upregulated biofilm production, transporter proteins for carbon source uptake, and proteins for fatty acid degradation to ensure energy generation. The strain's multiple stress responses work synergistically to resist low-temperature stress, ensuring its adaptability to low-temperature environments and ability to degrade E2. Finally, six genes related to survival at low temperature (identified in the transcriptome analysis) were expressed in E. coli BL21, and they were found to contribute to recombinant E. coli growth at low temperature.
研究领域:
微生物学
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环境科学
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分子生物学
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基因组学
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DOI
PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
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2024
·
IF 8.2
Meng Zhou,Zishu Liu,Baofeng Zhang,Baolan Hu
Arsenic and PAHs impose environmental stress on soil microorganisms, yet their compound effects remain poorly understood. While soil microorganisms possess the ability to metabolize As and PAHs, the mechanisms of microbial response are not fully elucidated. In our study, we established two simulated soil systems using soil collected from Xixi Wetland Park grassland, Hangzhou, China. The As-600 Group was contaminated with 600 mg/kg sodium arsenite, while the As-600-PAHs-30 Group received both 600 mg/kg sodium arsenite and 30 mg/kg PAHs (phenanthrene:fluoranthene:benzo[ a ]pyrene = 1:1:1). These systems were operated continuously for 270 days, and microbial responses were assessed using high-throughput sequencing and metagenomic analysis. Our findings revealed that compound contamination significantly promoted the abundance of microbial defense-related genes, with general defense genes increasing by 11.07 % ∼ 74.23 % and specific defense genes increasing by 44.13 % ∼ 55.74 %. The dominate species Rhodococcus adopts these general and specific defense mechanisms to resist compound pollution stress and gain ecological niche advantages, making it a candidate strain for soil remediation. Our study contributes to the assessment of ecological damage caused by As and PAHs from a microbial perspective and provides valuable insights for soil remediation.
研究领域:
环境科学
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微生物学
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PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2020
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IF 9.038
Shanshan Sun,Haizhen Wang,Kang Yan,Jun Lou,Jiahui Ding,Shane A. Snyder,Laosheng Wu,Jianming Xu
A highly eff ;ective phenanthrene (PHE)-degrading co-culture containing Rhodococcus sp. WB9 and Mycobacterium sp. WY10 was constructed and completely degraded 100 mg L −1 PHE within 36 h, showing improved degradation rate compared to their monocultures. In the co-culture, strain WY10 played a predominant role in PHE degradation. 1-hydroxy-2-naphthoic acid was an end-product of PHE degradation by strain WB9 and accumulated in the culture medium to serve as a substrate for strain WY10 growth, thereby accelerating PHE degradation. In turn, strain WY10 degraded PHE and 1-hydroxy-2-naphthoic acid intracellularly to form phthalate and protocatechuate that were exported to the culture medium through efflux transporters. However, strain WY10 cannot take up extracellular phthalate due to the absence of phthalate transporters, restricting phthalate degradation and PHE mineralization. In the co-culture, phthalate and protocatechuate accumulated in the culture medium were taken up and degraded towards TCA cycle by strain WB9. Therefore, the metabolic cross-feeding of strains WB9 and WY10 accelerated PHE degradation and mineralization. These findings exhibiting the synergistic degradation of PHE in the bacterial co-culture will facilitate its bioremediation application.
研究领域:
微生物学
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环境科学
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PubMed
高影响因子
Microorganisms
·
2022
·Vol. 11
·期 1
·67
·
IF 4.926
Kejian Tian,Yue Yu,Qing Qiu,Xuejian Sun,Fanxing Meng,Yuanping Bi,Jinming Gu,Yibing Wang,Fenglin Zhang,Hongliang Huo
Bisphenol A (BPA) pollution poses an increasingly serious problem. BPA has been detected in a variety of environmental media and human tissues. Microbial degradation is an effective method of environmental BPA remediation. However, BPA is also biotoxic to microorganisms. In this study,Rhodococcus equiDSSKP-R-001 (R-001) was used to degrade BPA, and the effects of BPA on the growth metabolism, gene expression patterns, and toxicity-resistance mechanisms ofRhodococcus equiwere analyzed. The results showed that R-001 degraded 51.2% of 5 mg/L BPA and that 40 mg/L BPA was the maximum BPA concentration tolerated by strain R-001. Cytochrome P450 monooxygenase and multicopper oxidases played key roles in BPA degradation. However, BPA was toxic to strain R-001, exhibiting nonlinear inhibitory effects on the growth and metabolism of this bacterium. R-001 bacterial biomass, total protein content, and ATP content exhibited V-shaped trends as BPA concentration increased. The toxic effects of BPA included the downregulation of R-001 genes related to glycolysis/gluconeogenesis, pentose phosphate metabolism, and glyoxylate and dicarboxylate metabolism. Genes involved in aspects of the BPA-resistance response, such as base excision repair, osmoprotectant transport, iron-complex transport, and some energy metabolisms, were upregulated to mitigate the loss of energy associated with BPA exposure. This study helped to clarify the bacterial mechanisms involved in BPA biodegradation and toxicity resistance, and our results provide a theoretical basis for the application of strain R-001 in BPA pollution treatments.Keywords:Bisphenol A;Rhodococcus;biodegradation;toxicity resistance
研究领域:
微生物学
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环境科学
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PubMed
高影响因子
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
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2018
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IF 3.562
Juping You,Mine Du,Han Chen,Xinying Zhang,Shihan Zhang,Jianmeng Chen,Zhuowei Cheng,Dongzhi Chen,Jiexu Ye
A new isolate identified as Rhodococcus sp. ZJUT312 via taxonomic and 16S rRNA analysis was used for the efficient degradation of benzene, toluene, ethylbenzene, and xylene (BTEX). The strain ZJUT312 was able to degrade all the BTEX. Their average biodegradation rates followed the order o -xylene > ethylbenzene > toluene > benzene > m -xylene > p -xylene. The degradation rate of o -xylene reached as high as 0.117 mmol L −1 h −1 , which was one to two orders of magnitude higher than that of all other reported o -xylene degrading bacteria. GC-MS analysis revealed that o -xylene degradation pathway mainly proceeded with 2-methylbenzylalcohol as an intermediate and CO 2 as a final product. Mass balance analysis of the carbon element indicated that approximately 59% the o -xylene carbons were transferred to cell biomass and about 20% were mineralized into CO 2 . Furthermore, the o -xylene degradation kinetics fitted well with Haldane's model. The maximum specific degradation rate (0.953 h −1 ) was approximately 2.25 times higher than the reported data in the literature.
研究领域:
环境生物学
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微生物学
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DOI
高影响因子
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
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2024
·
IF 4.1
Zheng-Fei Yan,Qing-Song Huang,Jing Yang,Xue-Yi Qiao,Bo Xu,Wei Xia,Ling-Qia Su
Microbial degradation is considered an effective and sustainable technique for the remediation of oily sludge; thus, the acquisition of crude oil-degrading bacteria is crucial for effective bioremediation. This study introduces a novel domestication-enrichment-isolation (DEI) strategy to isolate crude oil-degrading bacteria from oily sludge. Two strains, Rhodococcus rhodochrous JS-24 (R.rh) and Gordonia cholesterolivorans JS-13 (G.ch), demonstrated the highest degradation rates of 53.7% and 34.6%, respectively, within 7 days. While no synergistic effect was observed with their combined use in free bacterial consortia, and the overall degradation rate decreased to 51.9 %, which was weaker than that of R. rh treatment alone. The decrease in degradation rate is attributed to microbial flocculation towards crude oil: most droplets of crude oil were encapsulated into spherical aggregations by G. ch, thereby hindering the contact and degradation of droplets by R. rh. In contrast, immobilization technology significantly enhanced crude oil degradation by eliminating this flocculation effect. The immobilized bacterial consortium achieved a 95.5% degradation rate, representing the highest degradation rate reported for bacterial consortia. This study reveals for the first time that the side effects of bioflocculation on crude oil degradation and provides guidance for the construction of bacterial consortium.
研究领域:
环境微生物学
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污染治理
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生物修复
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DOI
高影响因子
ARCHIVES OF MICROBIOLOGY
·
2026
·Vol. 208
·期 5
·235
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IF 3.4
Zhou Yong,Wu Lei,Rubo Lv,Szpyrka Ewa,Podbielska Magdalena,Amirian Veghar,Russel Mohammad
This study investigated the aerobic biodegradation potential of two novel indigenous bacterial strains, Pseudomonas aeruginosa DUT-Pa and Rhodococcus erythropolis DUT-Re, utilizing benzene, toluene, ethylbenzene, and o-xylene (BTEX) as the sole carbon source. The optimal metabolic activity for both strains was identified at neutral pH (7.0) and mesophilic conditions (30 °C), establishing a critical baseline for enhancing bioremediation protocols. Biochemical oxygen demand (BOD) analysis revealed a direct correlation between the substrate concentration (up to 400 mg/L) and microbial respiratory activity. Dissolved oxygen (DO) depletion from 7.77 mg/L (pre-experiment) to 2.97 mg/L (DUT-Pa) and 2.15 mg/L (DUT-Re) further confirmed the oxygen-dependent degradation. In the gas phase, the highest degradation rate was recorded for benzene, with 98.43, 97.34, and 98.91% by DUT-Pa, DUT-Re, and mixed bacteria, respectively. Meanwhile, the liquid phase demonstrated superior toluene degradation efficiency by DUT-Pa, DUT-Re, and mixed bacteria with 91.99, 83.54, and 93.27% respectively. Bacterial combinations enhanced BTEX degradation, achieving the shortest half-lives and the highest degradation rate constants. Meanwhile, the SOD (325 U/mL) level and MDA (1.5 to 2.59 nmol/g) increased in the mixed system. This study demonstrates that an additive effect of DUT-Pa and DUT-Re combination promotes efficient, complete degradation of BTEX and offers a scalable, eco-friendly solution based on strain-specific cooperative microbial dynamics. Graphical
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高影响因子
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