FOOD MICROBIOLOGY
·
2025
·
IF 4.6
Jiashi Li,Zhong Lu,Xiaoli Zeng,Hanxiao Zhang,Haixia Lu,Lifang Feng,Junli Zhu
Quorum quenching through natural and nontoxic N -acyl homoserine lactonase (AHL-lactonase) has been regarded as a promising approach for inactivating QS-mediated bacterial spoilage. However, their poor catalytic performance remains a major challenge for practical application. To address these limitations, we developed an efficient rational design strategy for AHL lactonase AiiA to obtain a variant with high catalytic efficiency and a broad substrate spectrum, based on computer-aided structural analysis, molecular dynamics simulation, and energy calculation. Results showed that three highly flexible regions in AiiA were identified as vital sites to recognize and position different substrates, possessing high engineering potential. Among the obtained 10 mutants, AiiA A130T exhibited the strongest degradation against short-chain AHL (C 4 -HSL and C 6 -HSL), along with improved thermostability, compared to wild-type enzyme (AiiA WT ). In Pseudomonas fluorescens PF07, a majority of AHLs were quenched to undetectable levels by AiiA A130T , and the lactone ring of C 4 -HSL was verified to hydrolyze and produce form butyryl-L-homoserine. Its biofilm biomass, exopolysaccharides, exoprotein contents, and exoprotease activity were effectively repressed by 64.63 %, 48.86 %, 51.85 %, 61.50 % by AiiA A130T , respectively, in contrast with 46.51 %, 29.08 %, 23.55 %, 19.5 % by AiiA WT , without affecting bacterial growth. Moreover, the transcription levels of 16 crucial QS and biofilm-related genes in PF07 were dramatically downregulated ( P < 0.05), as evidenced by qRT-PCR. In contrast with the slight preservation for AiiA WT , AiiA A130T effectively retarded the fillet deterioration of large yellow croaker and extended their shelf life by 2 days. Overall, this study presents an efficient strategy for modifying AHL lactonase and yields a high-performance mutant, offering the application potential of AHL lactonase for controlling QS-mediated microbial spoilage of seafood.
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APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2026
·
IF 4.2
Haiqin Meng,Shun Pan,Zening Chai,Lixiang Zhou,Tianyu Zheng,Hanyu Zhang,He Fu,Lei Zou,Dongqi Liu,Jingcheng Dai,Dazhong Yan,Hong-Jun Chao
The catabolism of the priority environmental pollutant 2,4-xylenol requires bacteria to oxidize its ortho-methyl group. Its exact biochemical mechanism is uncharacterized until now. In this study, we resolve key metabolic bottlenecks in Pseudomonas putida NCIMB 9866. We demonstrate that functionally redundant Rieske oxygenase systems ensure the robust ortho-methyl oxidation of 2,4-xylenol. On the para-methyl oxidation branch, PchA2 acts as the main aldehyde dehydrogenase. It shows significantly higher catalytic efficiency than the previously reported PchA. Additionally, we characterized PmmA1B1, a newly identified three-component Rieske oxygenase system responsible for ortho-methyl oxidation, which is supported by two redundant isoenzymes (PmmA2B2 and PmmA3B3), by recruiting the shared endogenous ferredoxin Orf05169. The PmmA1B1-Orf05169 system catalyzes the successive oxidation of the ortho-methyl group of 4-hydroxy-3-methylbenzoate to a carboxyl group, yielding the high-value pharmaceutical precursor 4-hydroxyisophthalate. Structural and kinetic data revealed that the active site architecture of PmmA1 enables efficient successive oxidation, distinguishing it from isoenzymes PmmA2B2 and PmmA3B3 that, when coupled with Orf05169, catalyze only incomplete oxidation. Overall, these results complete the 2,4-xylenol catabolic pathway by defining the enzymes required for both para- and ortho-methyl oxidation. They also reveal functional redundancy as an adaptive feature of microbial aromatic degradation and establish Rieske oxygenases as biocatalysts for converting methylated aromatic pollutants into value-added chemicals.
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JOURNAL OF HAZARDOUS MATERIALS
·
2020
·
IF 9.038
Xuejun Wang,Hao Wu,Xiaoyu Wang,Haixia Wang,Kankan Zhao,Bin Ma,Zhenmei Lu
Dibutyl phthalate (DBP), widely used as plasticizer , is a typical soil contaminant. A new isolate, Arthrobacter nicotianae ZM05, is efficient at degrading DBP but lacks stress resistance to adverse environments. In this study, to isolate effective cooperators of strain ZM05 under pH stress and explore the effects of DBP on the bacterial community structure and interaction between bacteria, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacteria ZM05. 16S rRNA gene sequencing analysis showed that DBP contamination decreased microbial community diversity and weakened potential interactions between microorganisms , evidenced by fewer links, lower average degree, and lower average clustering coefficients in the cooccurrence network. Furthermore, the subnetworks showed that DBP shifted the interactions between strain ZM05 and other microbes. Based on the prediction of the network, the nondegrading bacterium Pseudomonas aeruginosa ZM03 was isolated and proven through coculture experiments to have a positive interaction with strain ZM05 during DBP degradation under pH stress. Strain ZM03 could utilize downstream acidic metabolites to alleviate acid inhibition and accelerate degradation. This study provides solid evidence that bacterial communities adjust their interactions to adapt to DBP stress and provides new insight into the prediction of microbes that are cooperative with degrading bacteria.
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Frontiers in Microbiology
·
2023
·
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.
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BIOSENSORS & BIOELECTRONICS
·
2019
·
IF 9.518
Xin Zhang,Guoming Xie,Dan Gou,Peng Luo,Yuan Yao,Hui Chen
Pseudomonas aeruginosa ( P. aeruginosa ) is one of the most intractable multidrug-resistant bacteria of nosocomial infections. The conventional detection methods for P. aeruginosa are time-consuming or low detection sensitivity. Here, a novel enzyme-free electrochemical biosensor was constructed to detect P. aeruginosa rapidly and sensitively. Firstly, the ZrMOF with large surface area was synthesized, which offers excellent adsorption. Further, it was connected with a specific amount of Cu 2+ to synthesize Cu-ZrMOF with high catalytic activity . Then the [email protected] @DNA nanocomposite was composed and served as the signal probe to catalyse the decomposition of H 2 O 2 . Moreover, high conductive Super P was introduced to increase the electron transfer for satisfactory detection sensitivity. The proposed biosensor was constructed and used to quantify P. aeruginosa with a wide linearity range of 10–10 6 CFU mL −1 and a low limit of detection of 2 CFU mL −1 (S/N = 3). Compared with conventional methods, the new method of present biosensor is more sensitive, and less time-consuming (only within 120 min). The analytical performance evaluation indicated that the biosensor exhibits good reproducibility and specificity. Finally, the biosensor was successfully applied to quantify P. aeruginosa in spiked urine samples. These results show that the proposed electrochemical biosensor might be a potential laboratory tool for detecting P. aeruginosa in the clinic.
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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2019
·
IF 3.571
Yu Zhang,Tengjie Li,Yuanfang Liu,Xiaoyan Li,Chunmei Zhang,Zhaozhong Feng,Xue Peng,Zongyun Li,Sheng Qin,Ke Xing
The biocontrol activity and chemical composition of the volatile organic compounds (VOCs) produced by Pseudomonas chlororaphis subsp. aureofaciens SPS-41 were investigated. The VOCs inhibited mycelial growth and spore germination in Ceratocystis fimbriata, which causes black rot disease in sweet potato tuber roots (TRs) and showed wide-spectrum antifungal activity against several plant pathogenic fungi. A microscopic examination of C. fimbriata cells suggested morphological changes and a loss of cellular contents. Different inoculation strategies significantly affected the antifungal activity of the VOCs. In the volatile profile of SPS-41, the most abundant compound, 3-methyl-1-butanol, followed by phenylethyl alcohol and 2-methyl-1-butanol showed strong inhibition toward C. fimbriata. The weight loss rate and disease severity of the TRs were significantly reduced in response to the VOCs emitted by SPS-41. The results suggest that the VOCs produced by P. chlororaphis subsp. aureofaciens SPS-41 might constitute an attractive biological fumigant for controlling black rot disease in sweet potato TRs.
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Microbial Cell Factories
·
2017
·Vol. 16
·期 1
·1-10
·
IF 3.681
Zhang Hui,Li Mengya,Li Jie,Wang Guangli,Liu Yuan
Quizalofop- p -ethyl (QPE) is a post-emergence herbicide that effectively controls grass weeds and is often detected in the environment. However, the biochemical and molecular mechanisms of QPE degradation in the environment remains unclear. In this study, a highly effective QPE-degrading bacterial strain J-2 was isolated from acclimated activated sludge and identified as a Pseudomonas sp., containing the QPE breakdown metabolite quizalofop acid (QA) identified by Liquid Chromatography-Ion Trap-Mass Spectrometry (LC-IT-MS n ) analysis. A novel QPE hydrolase esterase-encoding gene qpeH was cloned from strain J-2 and functionally expressed in Escherichia coli BL21 (DE3). The specific activity of recombinant QpeH was 198.9 ± 2.7 U mg −1 for QPE with K
m
and K
cat
values of 41.3 ± 3.6 μM and 127.3 ± 4.5 s −1 . The optimal pH and temperature for the recombinant QpeH were 8.0 and 30 °C, respectively and the enzyme was activated by Ca 2+ , Cd 2+ , Li + , Fe 3+ and Co 2+ and inhibited by Ni 2+ , Fe 2+ , Ag + , DEPC, SDS, Tween 80, Triton X, β-mercaptoethanol, PMSF, and pCMB. In addition, the catalytic efficiency of QpeH toward different AOPP herbicides in descending order was as follows: fenoxaprop-P-ethyl > quizalofop-P-tefuryl > QPE > haloxyfop-P-methyl > cyhalofopbutyl > clodinafop-propargyl. On the basis of the phylogenetic analysis and multiple sequence alignment, the identified enzyme QpeH, was clustered with esterase family V, suggesting a new member of this family because of its low similarity of amino acid sequence with esterases reported previously.
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WATER RESEARCH
·
2022
·
IF 13.4
Xin Qi,Hua Yin,Minghan Zhu,Pengling Shao,Zhi Dang
Biochar-assisted microbial degradation technology is considered as an important strategy to eliminate organic pollutants, but the mechanism of biochar in affecting biodegradation has not been systematically studied. To address this knowledge gap, the effect of various biochars on biodegradation of different initial concentrations of BDE-47 by Pseudomonas plecoglossicida was investigated. The results showed that biochar exhibited significant promotion to the biodegradation of BDE-47, especially at concentrations of BDE-47 above 100 μg/L. The promotion effect was negatively influenced by the aromaticity and micropore volume of biochar. Biochar alleviated the cytotoxicity of BDE-47 to P. plecoglossicida and promoted cell proliferation based on toxicity assays. Additionally, biochar acted as shelter and stimulated the secretion of extracellular polymeric substances, which might support P. plecoglossicida to struggle with extreme conditions. Metabolomic analysis indicated that biochar resulted in upregulation expression of 38 metabolites in P. plecoglossicida . These upregulated metabolites were mainly related to glyoxylate and dicarboxylate metabolism, citrate cycle, and serial amino acid metabolism, suggesting that biochar could improve the BDE-47 biodegradation via enhancing oxidative metabolism and energy supply of the bacterial cells. This work elucidates how biochar can affect BDE-47 biodegradation and provides insights for the application prospect of biochar-assisted microbial degradation technology in the environment.
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iScience
·
2022
·
IF 6.107
Shixun Liu,Anming Xu,Bin Xie,Fengxue Xin,Weiliang Dong,Jie Zhou,Min Jiang
Summary The synthesis of biofilm exopolysaccharides and rhamnolipids (RLs) are two interrelated processes in Pseudomonas aeruginosa , but how bacteria coordinate these two processes remains unclear. We collected a P. aeruginosa KT1115 with rugose small colony variant (RSCV) phenotype from soil, and used it to study the dynamic regulation mechanism of biofilm polysaccharide and RLs synthesis. The results showed that the overproduction of biofilm exopolysaccharides at biofilm stage ultimately contributed the surge of RLs production at RLs stage. This phenomenon was further verified by comparing PAO1 with its engineered RSCV mutant, PAO1Δ wspF . Further genomic, transcriptomic analyses and gene deletion revealed that downregulation of c-di-GMP level was the key to switch biofilm exopolysaccharides accumulation to RLs surge, by transcriptionally upregulating a c-di-GMP phosphodiesterase NbdA. Overall, this study demonstrates the importance of c-di-GMP in coordinating biofilm exopolysaccharides and RLs synthesis, and provides an inspiration for enhancing RLs production through regulating c-di-GMP level.
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Journal of Environmental Chemical Engineering
·
2025
·
IF 7.2
Mengyao Gui,Hongwei Yang,Erming Ouyang
Polystyrene nanoplastics (NPs), ubiquitous contaminants in aquatic ecosystems, are known to impede conventional anoxic denitrification processes. However, their effects on aerobic denitrification systems remained poorly understood. This study systematically elucidates the mechanistic interactions between polystyrene NPs and aerobic denitrification performance. Results revealed polystyrene NPs caused concentration-dependent suppression of denitrification efficiency in the aerobic denitrifier Pseudomonas stutzeri PCN-1 under controlled laboratory conditions (aerobic, 30 ℃). At NPs concentrations escalating from 100 to 1000 μg L⁻¹ , nitrate removal rates decreased markedly (0.4–3.3 mg L⁻¹ h⁻¹), paralleled by progressive accumulation of nitrite (8.8–87.2 mg L⁻¹) and N₂O (31.2–58.3 mg L⁻¹). Mechanistic analyses revealed that polystyrene NPs induced biotoxic effects through two primary pathways: (1) disruption of cellular membrane integrity and (2) excessive generation of reactive oxygen species (ROS), collectively impairing bacterial viability and metabolic activity. Furthermore, critical denitrification processes were compromised, including diminished electron transport system activity, reduced catalytic activities of key denitrification enzymes, and downregulation in transcriptional expression of functional genes (e.g. napA , nirS , cnorB , and nosZ ). These multilevel inhibitions collectively contributed to the observed deterioration in nitrogen removal capacity. This investigation provides novel insights into the ecotoxicological risks posed by NPs to microbial nitrogen cycling in aquatic environments.
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Drug Delivery and Translational Research
·
2026
·
IF 6.9
Ran Fang,Chai Guihong
Pseudomonas aeruginosa (PA) biofilm-associated chronic lung infections pose a significant therapeutic challenge due to the limited penetration and efficacy of conventional antibiotics. In this study, we developed an innovative dry powder inhaler (DPI) formulation co-loading ciprofloxacin-encapsulated liposomes (CIP-Lips) and S-nitrosoglutathione (GSNO) using an ultrasonic spray-freeze-drying (USFD) technique. GSNO, a nitric oxide (NO) donor, promotes biofilm dispersion and induces bacterial phenotypic switching, thereby enhancing the accessibility of CIP-Lips to biofilm-embedded bacteria. Subsequently, CIP released from the liposomes exerts direct antibacterial activity. The combination of CIP-Lips and GSNO produces a synergistic “biofilm-disrupting and bactericidal” therapeutic effect, leading to effective biofilm eradication. The optimized DPI formulation exhibited satisfactory in vitro aerosol performance, with a fine particle fraction of 36.51 ± 0.49%, ensuring efficient lung deposition. In vitro evaluations further confirmed pronounced biofilm disruption and bactericidal efficacy. Furthermore, in a murine model of chronic pulmonary infection, the CIP-Lips/GSNO DPI significantly reduced the bacterial burden without observable systemic toxicity. This inhalable system represents a promising strategy for the treatment of PA biofilm-associated lung infections.
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ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2022
·Vol. 29
·期 32
·48638-48647
·
IF 5.19
Li Qian,Tang Zeqin,Zhang Jiahui,Hu Jingtao,Chen Jianmeng,Chen Dongzhi
Simultaneous biodegradation of malodorous 1-propanethiol (PT) and dimethyl sulfide (DMS) by Pseudomonas putida S-1 and Alcaligenes sp. SY1 was investigated and the interactions implicated were explored. Results showed that PT was completely degraded in 33 h, while a lag of 10 h was observed for DMS degradation alone, and the lag was even extended to 81 h in the binary mixture. Mechanism analysis found that the lag was mainly attributed to the exposure of DMS degrader ( Alcaligenes sp. SY1), rather than PT metabolites and PT degrader. The exposure time and PT concentration also influenced the lag duration much. Citric acid could effectively reduce the lag. Pseudo-first-order model was proved suitable for the description of PT degradation, revealing that PT degradation could be enhanced in presence of DMS with a concentration of < 50 mg L −1 . A modified Gompertz model, incorporated the lag phase, was developed for the description of DMS degradation in the mixture, revealing that DMS degradation depended on the initial PT concentration, and when the lag was not considered, PT with low-concentration could promote DMS biodegradation, while a higher concentration (> 20 mg L −1 ) cast negative effect.
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