JOURNAL OF HAZARDOUS MATERIALS
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2022
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IF 14.224
Jiangqiao Bao,Jibing Li,Longfei Jiang,Weiping Mei,Mengke Song,Deyin Huang,Chunling Luo,Gan Zhang
Biochar has been widely used for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but its mechanism of influencing PAH biodegradation remains unclear. Here, DNA-stable isotope probing coupled with high-throughput sequencing was employed to assess its influence on phenanthrene (PHE) degradation, the active PHE-degrading microbial community and PAH-degradation genes (PAH-RHD α ). Our results show that both Low-BC and High-BC (soils amended with 1 % and 4 % w/w biochar, respectively) treatments significantly decreased PHE biodegradation and bioavailable concentrations with a dose-dependent effect compared to Non-BC treatment (soils without biochar). This result could be attributed to the immobilisation of PHE and alteration of the composition and abundance of the PHE-degrading microbial consortium by biochar. Active PHE degraders were identified, and those in the Non-BC, Low-BC and High-BC microcosms differed taxonomically. Sphaerobacter , unclassified Diplorickettsiaceae , Pseudonocardia , and Planctomyces were firstly linked with PHE biodegradation. Most importantly, the abundances of PHE degraders and PAH-RHD α genes in the 13 C-enriched DNA fractions of biochar-amended soils were greatly attenuated, and were significantly positively correlated with PHE biodegradation. Our findings provide a novel perspective on PAH biodegradation mechanisms in biochar-treated soils, and expand the understanding of the biodiversity of microbes involved in PAH biodegradation in the natural environment.
研究领域:
环境科学
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微生物学
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DOI
PubMed
高影响因子
CHEMOSPHERE
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2019
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IF 5.108
Minbo Qi,Hui Huang,Ying Zhang,Haixia Wang,Hanbo Li,Zhenmei Lu
Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. ( Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella , Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79–93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.
研究领域:
环境科学
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微生物学
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基因组学
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DOI
PubMed
高影响因子
Water
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2024
·Vol. 16
·期 17
·2537
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IF 3
Bo Li,Hulong Liu,Xiaona Liu,Li Han,Jing Yang,Lingke Kang,Liuyuan Tang,Tianwei Qian
Bioremediation is a promising technique owing to its effectiveness, low cost, and environmental friendliness. Previous studies have focused on the degradation efficiency of polycyclic aromatic hydrocarbons (PAHs) in soil and water. However, the expression of PAH-catabolic genes in organisms involved in the degradation process has been rarely and unsystematically reported. In this study, a PAH-degrading strain—Pseudomonas aeruginosa(PQ249631)—was successfully isolated from coking-contaminated soil and used for PAH degradation in soil and water. Furthermore, the degradation of PAHs (naphthalene, fluorene, phenanthrene, anthracene, and pyrene) was investigated in single, binary, and mixture systems to explore the interaction of substrates. The results showed that when naphthalene was used as a cometabolite carbon source, the removal rates of fluorene, phenanthrene, anthracene, and pyrene increased from 14.33%, 17.25%, 6.61%, and 4.47% to 72.08%, 100.00%, 15.63%, and 6.63%, respectively. In a PAH mixture, the degradation rate of each PAH was higher when naphthalene, rather than glucose, was used as the cometabolite carbon source. Transcriptome analysis revealed significant differential expression of PAH-catabolic genes and ATP-binding cassette transporter-related genes under naphthalene stress. The enhanced degradation of PAHs could be attributed to the augmentation of the PAH metabolic pathway and membrane transportation, facilitating the transfer of PAHs to bacteria. These findings underscore the effectiveness ofP. aeruginosaas a PAH degrader and provide molecular insights into enhancing PAH degradation.
研究领域:
环境科学
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微生物学
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生物修复
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基因组学
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DOI
高影响因子
Polymers
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2018
·Vol. 10
·期 10
·1080
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IF 2.935
Ju-Hui Zhang,Hui-Zhen Yang,Ji Zhang,Yan-Hong Liu,Xi He,Ya-Ping Xiao,Xiao-Qi Yu
The linking and modification of low molecular weight cationic polymers (oligomers) has become an attracted strategy to construct non-viral gene carriers with good transfection efficiency and much reduced cytotoxicity. In this study, PEI 600 Da was linked by biodegradable bridges containing rigid aromatic rings. The introduction of aromatic rings enhanced the DNA-binding ability of the target polymers and also improved the stability of the formed polymer/DNA complexes. The biodegradable property and resulted DNA release were verified by enzyme stimulated gel electrophoresis experiment. These materials have lower molecular weights compared to PEI 25 kDa, but exhibited higher transfection efficiency, especially in the presence of serum. Flow cytometry and confocal laser scanning microscopy results indicate that the polymers with aromatic rings could induce higher cellular uptake. This strategy for the construction of non-viral gene vectors may be applied as an efficient and promising method for gene delivery.Keywords:non-viral vectors;gene delivery;polyethylenimine;structure–activity relationship
研究领域:
遗传学
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生物技术
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药学
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产品关联
DOI
PubMed
高影响因子
MICROCHEMICAL JOURNAL
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2025
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IF 5.1
Qinghao Song,Zhihao Huang,Ying Xiao,Yu Zhang,Liyi Li,Yi Yu,Si Chen,Qing Wu
MXene Ti 3 C 2 has emerged as a promising biosensing material due to the high surface area, excellent biocompatibility, tunable functional groups (-F, O, -OH), and outstanding electrical conductivity, effectively addressing issues such as low sensitivity and inadequate biocompatibility in sensors. This work, MXene Ti 3 C 2 -AuNPs are synthesized as functional materials through a one-step synthesis method. We propose the first all-fiber biosensor featuring a laterally offset SMF-MMF-SMF-MMF-SMF (SMSMS) interferometric structure functionalized with MXene Ti 3 C 2 -AuNPs as the substrate of the biosensor sensor device, for the detection of the alkane degradation (ALK) gene, to the best of our knowledge. The biosensor enables in-situ target DNA (tDNA) detection across 1 fM to 1 μM concentrations based on this nanoengineered interface, demonstrating 1755.95 nm/RIU sensitivity and a 1 fM limit of detection (LOD) – Two orders of magnitude lower than conventional optical DNA sensors (μM-level). The sensor exhibits a wavelength shift of 1.23 nm in response to complementary DNA, which is 8.2 times greater than that for non-complementary DNA, with a maximum wavelength shift error of 0.11 nm across three repeated experiments and a shift within 0.1 nm over 7 days for sensors with attached functional MXene Ti 3 C 2 , demonstrating excellent specificity, stability, and reproducibility. These advantages render the fiber optic device coated with MXene Ti 3 C 2 -AuNPs an effective solution for ALK gene monitoring and broaden its applicability for ultra-trace DNA detection in environmental and biomedical contexts
研究领域:
生物传感器
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纳米技术
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光学传感
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分子生物学
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环境监测
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生物医学工程
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产品关联
DOI
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2020
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IF 9.038
Ning Hou,Qiaoruo Wang,Yang Sun,Xianyue Li,Qiuying Song,Xinxin Jiang,Baoxin Li,Xinyue Zhao,Hailian Zang,Dapeng Li,Chunyan Li
In recent years, special attention has been devoted to biodemulsifiers as a new type of environment-friendly demulsifiers. A novel biodemulsifying oxalate decarboxylase (OxdC) secreted by Bacillus mojavensis XH1 is reported in the present study. A genome-wide comparison showed that strains with high demulsification efficiencies all possess alkane degradation genes. An analysis of the differentially expressed genes and proteins induced by different substrates showed that OxdC secreted by XH1 was an effective demulsifier. Moreover, the demulsification ability was verified by prokaryotic gene expression, knockout and complementation analyses. OxdC from XH1 exhibited a strong demulsification capacity and significantly outperformed the model protein Bacillus subtilis 168 OxdC (Yvrk), which shared a high amino acid similarity but showed limited demulsification ability. Based on a comparison of the structural characteristics, the hydrophobic amino acids on the surface of OxdC were identified as a key factor driving the favorable demulsification activity of XH1. The metabolic pathways of XH1 used liquid paraffin and glucose as substrates, illustrating that hydrocarbons are necessary for biodemulsifier secretion. The present study provides new insight into the application of OxdC as an additional genetic resource in biodemulsification.
研究领域:
微生物学
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环境生物技术
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生物化学
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基因组学
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产品关联
DOI
PubMed
高影响因子
Microbial Biotechnology
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2024
·Vol. 17
·期 2
·e14415
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IF 4.8
Zhikuan Wang,Hailiang Qiu,Yulong Chen,Xuemin Chen,Chunhua Fu,Longjiang Yu
Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK-90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK-90 involves the selective removal of 5,6-spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG-1 and SCG-2, in the genome of strain HK-90. SCG-1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m-∆kstD1 converting phytosterols to intermediate 9α-hydroxyandrostenedione (9-OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG-2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG-2 resulted in the conversion of diosgenin to 9-OHAD and 9,16-dihydroxy-pregn-4-ene-3,20-dione (9,16-(OH) 2 -PG) in mutant m-ΔkstD2 . Moreover, the engineered strain mHust-ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9-OHAD by metabolizing phytosterols, and accumulate 9-OHAD and 9,16-(OH) 2 -PG from diosgenin. Diosgenin catabolism in strain mHust-ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16-(OH) 2 -PG, and 9-OHAD to 9α-hydroxytestosterone (9-OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21-carbon and 19-carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism.
研究领域:
生物技术
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微生物学
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生物化学
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药学
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产品关联
DOI
PubMed
高影响因子
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