APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
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2021
·Vol. 105
·期 7
·2841-2854
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IF 4.813
Zhou Gang,Wang Ying-si,Peng Hong,Li Su-juan,Sun Ting-li,Shen Peng-fei,Xie Xiao-bao,Shi Qing-shan
Abstract The genus Citrobacter is commonly found in environmental and industrial settings, some members of which have been used for bioremediation of heavy metals owing to the absorption ability of their biofilms. Although our previous studies have found that the outer membrane protein A (OmpA) contributes to the process of Citrobacter werkmanii biofilm formation, the underlying mechanisms remain elusive. Therefore, we deleted ompA from the genome of C. werkmanii and investigated its phenotypes in comparison to the wild type strain (WT) and the complementary strain using biochemical and molecular techniques including RNA-Seq. Our results demonstrated that the deletion of ompA led to an increase in biofilm formation on both polystyrene and glass surfaces due to upregulation of some biofilm formation related genes. Meanwhile, swimming ability, which is mediated by activation of flagellar assembly genes, was increased on semi-solid plates in the ∆ompA strain when compared with WT. Additionally, inactivation of ompA also caused increased 1,2-benzisothiazolin-3-one (BIT) resistance, differential responses to Ca 2+ stress, curli protein expression and cellulose production. Finally, ∆ompA caused differential expression of a total of 1470 genes when compared with WT, of which 146 were upregulated and 1324 were downregulated. These genes were classified into different Gene Ontology (GO) and KEGG pathways. In summary, ompA in C. werkmanii contributes to a variety of biological functions and may act as a target site to modulate biofilm formation. Key points
• ompA is a negative regulator for biofilm formation by C. werkmanii.
• ompA inhibits swimming motility of C. werkmanii.
• ompA deletion causes different expression profiles in C. werkmanii.
研究领域:
微生物学
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分子生物学
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环境科学
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PubMed
高影响因子
CHEMOSPHERE
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2014
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IF 3.499
Feng Li,Lizhong Zhu
The effects of the surfactants, Tween 80 and sodium dodecyl benzene sulfonate (SDBS) on a membrane’s fatty acid composition and the transmembrane transport of phenanthrene were investigated. The results indicated that both surfactants could modify the composition of fatty acids of Citrobacter sp. Strain SA01 cells, 50 mg L −1 of both surfactants changed the composition of the fatty acids the most, increasing the amount of unsaturated fatty acids. The comparison of fatty acid profiles with diphenylhexatriene fluorescence anisotropy, a probe for plasma membrane fluidity, suggested that an increased amount of unsaturated fatty acids corresponded to greater membrane fluidity. In addition, increased unsaturated fatty acids promoted phenanthrene to partition from the extracellular matrix to cell debris, which increased reverse partitioning from the cell debris to the cytochylema. The results of this study were expected in that the addition of a surfactant is a simple and effective method for accelerating the rate-limiting step of transmembrane transport of hydrophobic organic compounds (HOCs) in bioremediation.
研究领域:
环境微生物学
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污染修复
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DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2022
·
IF 14.224
Xingxing Peng,Tianyu Li,Qihang Zheng,Yingyuan Lu,Yuzhe He,Yetao Tang,Rongliang Qiu
Hexabromocyclododecane (HBCD) is a typical persistent organic pollutant that is widely detected in the environment. Despite the significant efforts put into its mineralisation , there is still a lack of microorganism resources that can completely mineralise HBCD. Stable isotope analysis revealed that the Citrobacter sp . Y3 can use [ 13 C]HBCD as its sole carbon source and degrade or even mineralise it into 13 CO 2 , with a maximum conversion rate of 100% in approximately 14 days. Strain Y3 could completely mineralise HBCD, which it used as its only carbon source, and six debromination enzymes related to HBCD degradation were found in Y3, including haloalkane dehalogenase (DhaA), haloacid dehalogenase (HAD), etc. A functional gene named HBCD-hd-1 , encoding a HAD, was found to be upregulated during HBCD degradation and heterologously expressed in Escherichia coli . Recombinant E. coli with the HBCD-hd-1 gene transformed the typical intermediate 4-bromobutyric acid to 4-hydroxybutanoic acid and showed excellent degradation performance on HBCD, accompanied by nearly 100% bromine (Br) ion generation. The expression of HBCD-hd-1 in Y3 rapidly accelerated the biodegradation of HBCD. With HBCD as its sole carbon source, strain Y3 could potentially degrade HBCD, especially in a low-nutrient environment.
研究领域:
环境科学
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微生物学
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分子生物学
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DOI
PubMed
高影响因子
CHEMICAL ENGINEERING JOURNAL
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2022
·
IF 16.744
Tianzhi Jin,Yajing Wang,Shun Yao,Chuxiao Hu,Ting Ma,Wenjie Xia
Carbon dioxide as a feedstock for synthesizing chemicals and fuels attracts numerous efforts via biological or chemical approaches. A newly Citrobacter BD11 was detected with distribution of 71.31 % in reservoir samples by metagenomic sequencing, and can convert CO 2 to succinic acid with hydrogen production under anaerobic condition. The pathway of hydrogen production and the succinic acid synthesis was explored by whole-genome sequencing and real-time quantitative polymerase chain reaction. The results showed the positive influences of pH, hydrogen pressure and magnesium ions on succinic acid production. The stage transition of hydrogen production and utilization was detected, and the nonlinear relationship between succinic acid production and exogenous carbon dioxide was proved. Under optimized conditions, the carbon fixation rate of 1.77 g/L*d and the succinate production rate of 7.51 g/L*d were finally achieved at pH = 7.0 with 50 KPa of hydrogen pressure and 4.0 g/L of MgCl 2 . This study demonstrated that this Citrobacter could be a promising platform for hydrogen production and convert CO 2 to diverse acids.
研究领域:
生物技术
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环境科学
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微生物学
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生物化学
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DOI
高影响因子
GENE
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2022
·
IF 3.913
Gang Zhou,Ying-si Wang,Hong Peng,Su-juan Li,Ting-li Sun,Cai-ling Li,Qing-shan Shi,Xiao-bao Xie
Citrobacter werkmanii , an aerobe and mesophilic Proteobacterium, is universal in industrial putrefaction, coastal water, and human blood. Our previous studies have discovered that outer membrane protein X (OmpX) of C. werkmanii is involved in calcium response, but the underlying mechanisms and its molecular characteristics remain elusive. To that end, the ompX gene was deleted from the genome of C. werkmanii and its phenotypic variations were thoroughly investigated in conjunction with the wild type (WT) and complementary strains using biochemical and molecular techniques such as RNA-Seq, respectively. The results demonstrated that deleting ompX reduces biofilm formation on polystyrene and glass surfaces. Meanwhile, Δ ompX ’s swimming ability but not for its twitching or swarming abilities, was also reduced on semi-solid plates compared with WT, which was caused by inhibition of flagellar assembly genes, such as flgC , flhB , and fliE , etc. Furthermore, ompX inactivation altered susceptibility to various bactericide classes, as well as responses to Ca 2+ and Mg 2+ stress. In addition, when compared to WT, Δ ompX captures a total of 1,357 deferentially expressed genes (DEGs), of which 465 were up-regulated and 892 were down-regulated, which can be enriched into various GO ontology and KEGG pathway terms. Furthermore, ompX , as well as ompD and ompW , can be modulated at the transcriptional levels by rbsR and tdcA . Overall, the ompX gene contributed to a variety of biological functions in C. werkmanii and could be served as a targeted site for controlling biofilm formation and developing new bactericides.
研究领域:
微生物学
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分子生物学
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基因组学
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生物信息学
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PubMed
高影响因子
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2023
·Vol. 30
·期 36
·85558-85568
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IF 5.8
Jin
Jingnan,Shi Yahui,Zhang Baozhong,Wan Dongjin,Zhang Qingye
A bacterial strain Citrobacter sp. HJS-1 was discovered from the sludge in a drainage canal of a coal mine. Firstly, its biodegradation capacity for benzo[a]pyrene (BaP) was detected under different concentrations. The results proved that the strain possessed excellent biodegradation capacity for BaP with high-efficiency degradation rates ranging from 78.9 to 86.8%. The highest degradation rate was observed in the low-concentration sample, and the high-concentration BaP had a slight influence on the biodegradation capacity due to the potential toxicity of BaP and its oxygen-containing derivatives. Meanwhile, the degradation test for the other five aromatic hydrocarbons (2- to 4-ring) proved that the strain had a comprehensive degradation potential. To clarify the biodegradation mechanism of BaP, a dioxygenase structure was constructed by homology modeling. Then, the interactions between dioxygenase and BaP were researched by molecular simulation. Combined with the identification of the vital BaP-cis-7,8-dihydrodiol intermediate and the interaction analysis, the initial oxidation mode and the binding site of BaP were revealed in the dioxygenase. Taken together, this study has offered a way to understand the biodegradation process of BaP and its interaction mechanism based on experimental and theoretical analysis.
研究领域:
环境微生物学
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生物化学
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分子生物学
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DOI
PubMed
高影响因子
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
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2019
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IF 4.527
Jinghao Wang,Sijing Bi,Yuancai Chen,Yongyou Hu
Gram-negative Citrobacter freundii with high Pd (II) reduction capacity was isolated from electroplating wastewater, and the electron transfer involved in Pd (II) bio-reduction by C. freundii JH was investigated in phosphate buffer saline solution with sodium formate as sole electron donor under anaerobic condition . FTIR spectra indicated that hydroxyl and amine groups on cell wall participated Pd (II) bio-sorption. TEM , XRD, XPS results confirmed that Pd (0) nanoparticles (NPs) could be bio-synthesized intra/extracellularly. Meanwhile, pH turn-over were observed owing to the reduction of cytochrome c (c-Cyt) in bio-reduction process. EPR spectra indicated that free radicals ( OH) was generated from high concentration Pd (II), which would cause seriously damage to cell. Despite of the lower tolerance to Pd (II), the cells at logarithmic phase exhibited higher Pd (II) reduction capacity (72.21%) than that at stationary phase (56.21%), which might be related to the relatively stronger proton motive force (PMF) created by the substrate oxidation and the electron transfer, as evidenced by electrochemical experiments (CV, DPV, amperometric I-t curves) and protein denaturalization experiments. Additionally, c-Cyt and riboflavin were confirmed to be important participants in electron transfer. Finally, a putative synthesis mechanism of Pd (0)-NPs was deduced. This study contributed to further understanding the electron transfer in Pd (II) reduction, and provided more information for the bio-synthetic of metal nanoparticles.
研究领域:
环境微生物学
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生物技术
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纳米技术
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微生物生物化学
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产品关联
DOI
PubMed
高影响因子
CURRENT ISSUES IN MOLECULAR BIOLOGY
·
2026
·Vol. 48
·期 8
·765
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IF 4.1
Pengji Zhou,Xingyu Liu,Bingqi Li,Lili Yang,Xianya Wu,Xizi Long,Fei Yang
To address the issues of low degradation efficiency in anaerobic bacteria targeting microcystin-LR (MC-LR) and the limitations of traditional genetic modification methods, this study applied ARTP mutagenesis technology for the first time to genetically engineer anaerobic MC-LR-degrading bacteria using theCitrobactersp. D03 isolated from Lake Taihu sediments as the parental strain. Through three rounds of ARTP-induced mutagenesis and directed screening, a highly efficient mutant, C29, was obtained. The results indicate that the optimal mutagenesis conditions are 60 s, with a lethality rate of 90.15%; the anaerobic degradation efficiency of MC-LR by mutant strain C29 was 14% higher than that of the wild-type strain, and the genetic efficiency remained stable after consecutive passages. Whole-genome resequencing of the new strain C29 revealed 10 mutation sites, involving key genes such astoxD,cheA,murI, andmobB. qRT-PCR validation showed that the expression of genes related to sulfur metabolism, cell wall synthesis, molybdenum cofactor synthesis, and environmental adaptation was significantly upregulated. The study confirms that ARTP mutagenesis can effectively enhance the degradation capacity of anaerobic degrading bacteria toward MC-LR through polygenic synergistic regulation, providing both microbial resources and a theoretical basis for in situ anaerobic bioremediation of MC-LR pollution in eutrophic water bodies.
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DOI
高影响因子
Environmental Technology & Innovation
·
2025
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IF 7.1
Xueping Jiang,Hao Li,Jia Kong,Yongjun Zang,Yuqi Li,Jianglong He,Ran Zhang,Bangxing Han,Kwang Sik Lee,Byung Rae Jin,Zhongzheng Gui
Chloramphenicol (CAP), a widely used antibiotic, persists in the environment and poses ecological risks. Despite the growing understanding of these degradation pathways of CAP, the secondary metabolic routes and their impacts on the environment remain poorly understood. Here, we aimed to characterize the CAP-biodegradation capability of a novel bacterial strain, evaluate the biodegradation kinetics of CAP under different nutritional and environmental conditions, and assess the toxicity of CAP and its degradation products. Citrobacter freundii CT2 isolated from fermented silkworm excrement was found to degrade CAP with an efficiency of 96.29 % within 24 h. CAP is the sole source of carbon, nitrogen, and energy for this bacterium. The degradation process fitted well with the first-order kinetics model. Ten potential biotransformation products were identified using ultraperformance liquid chromatography–high-resolution mass spectrometry (UPLC-HRMS) and high-performance liquid chromatography (HPLC), and five distinct metabolic pathways (acetylation, propionylation, butyrylation, dehydration, and oxidation) were predicted. A toxicity assessment of the biotransformation products, conducted using biological indicators, showed that the final metabolites were non-toxic to the environment, confirming that the biodegradation process resulted in detoxification. Bio-enhancement studies further demonstrated that strain CT2 effectively degraded CAP in wastewater. Genomic analysis showed that genes related to acetylation, propionylation, nitro reductase, and dehydrogenation in strain CT2 might be involved in the biodegradation of CAP. These results offer new insights into the diversity of CAP-degrading pathways and highlight the utility of strain CT2 as a potential bioremediation agent for CAP-contaminated environments.
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DOI
高影响因子
BIORESOURCE TECHNOLOGY
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2025
·
IF 9
Jian Gao,Jingyu Wu,Yuancai Chen
This study found that bio-Pd 0 nanoparticles could launch proton motive force (PMF)-mediated antibiotics efflux pump (AEP) to confer the detoxification capability on Citrobacter freundii , as evidenced by the highest sulfamethoxazole (SMX) specific degradation rate (81.7 μg L −1 mg −1 protein d −1 ) at high PMF (pH 6). The batch experiment and RT-qPCR results indicated that bio-Pd 0 activated the AcrB efflux pump through upregulating the AEP transcriptional regulation factor ramA (2.7–3.1 times), which benefited the intra/extracellular respiration and ATP production/utilization. Path analysis revealed that the prosperity of metabolic activity and extracellular electron output capacity enabled SMX biodegradation, mainly through the electron redistribution and energy optimization with the formate dehydrogenase/hydrogenase based Short-chain (FDH/Hase-S-chain). The upregulation of hypE (2.7–8.6 times) and atpD (1.9–2.3 times) genes encoding the Hase respiratory chain and the F-type ATP synthase, respectively, further supports this mechanism. These novel findings provided a new strategy to improve the biodegradation efficiency of antibiotics wastewater.
研究领域:
微生物学
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环境科学
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DOI
PubMed
高影响因子
Cell Reports
·
2025
·
IF 6.9
Weiben Xu,Ying Zhou,Haiying Ding,Mengqian Ye,Shujing Li,Linwei Xu,Xiangyu Jin,Zhajun Zhan,Lulu Song,Yuhua Zhang,Canming Wang,Zhengqin Zhu,Liefeng Ma,Libin Pan,Luo Fang
Pancreatic cancer is highly malignant, and while fluoropyrimidines (5-fluorouracil [5-FU] and capecitabine) are critical first-line treatments for metastatic cases, drug resistance remains a major challenge. In this study, we identified an association between Citrobacter enrichment in pancreatic tumors and poor overall survival in patients with pancreatic cancer, particularly in patients receiving fluoropyrimidine-based treatment. Co-culture of 5-FU with the Citrobacter freundii strain isolated from pancreatic cancer and intratumoral injection of this strain in xenograft models significantly reduce the antitumor efficacy of 5-FU. Subsequent analyses using mass spectrometry, bioinformatics, and gene knockout experiments revealed that C. freundii strain inactivates 5-FU via the PreTA, which is homologous to human dihydropyrimidine dehydrogenase (DPD). Gimeracil, a DPD inhibitor, preserves the efficacy of 5-FU by blocking PreTA activity. Other preTA -harboring bacteria also metabolized 5-FU, indicating broader bacteria-mediated 5-FU resistance. These findings reveal a potential microbiome-driven mechanism of chemotherapy failure and identify PreTA as a druggable target.
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DOI
PubMed
高影响因子
Journal of Functional Foods
·
2024
·
IF 3.8
Jinping Wang,Jianmin Wu,Zishen Lin,Ning Ma,Zhaoyue Men,Chao Zhang,Xi Ma,Hongyu Zheng
The invasion of pathogens derived from diet or the environment triggers intestinal inflammation, which is a result of the host intestinal barrier damage and immune dysfunction, such as the decrease of host defense peptides (HDPs) and inhibition of cell proliferation. Herein, the siRNA interference demonstrated that a critical lysozyme, which was mainly induced by dietary supplementations of sodium butyrate and forskolin, improved cell proliferation by inhibiting p38 MAPK and JNK signaling pathways and reinforced the intestinal barrier. Moreover, we established a mouse model of intestinal inflammation with Citrobacter rodentium ( C. rodentium ). It was found that NaBu and FSK stimulated intestinal epithelial proliferation to repair barrier damage, and performed stronger disease resistance to C. rodentium infection on account of the lysozyme upregulation in colon. Therefore, this study revealed that NaBu and FSK prevented or alleviated the development of foodborne infections by promoting lysozyme expression, which may be mediated by the effect of lysozyme on promoting cell proliferation and improving barrier function.
研究领域:
胃肠病学
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免疫学
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分子生物学
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微生物学
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DOI
高影响因子
危险品化学品经营许可证（带存储）