Frontiers in Microbiology
·
2022
·
IF 6.064
Wang Guangli,Li Xiang,Zheng Jiaxin,Li Xuedong,Bai Lingling,Yue Wenlong,Jiang Li
Diazinon is one of the most widely used organophosphate insecticides, one that is frequently detected in the environment. In this study, a diazinon-degrading bacterium, DI-6, previously isolated from diazinon-contaminated soil in China has been subsequently identified as Sphingobium sp. on the basis of its physiological and biochemical characteristics, as well as by virtue of a comparative analysis of 16S rRNA gene sequences. This strain is capable of using diazinon as its sole carbon source for growth and was able to degrade 91.8% of 100 mg L–1 diazinon over a 60-h interval. During the degradation of diazinon, the following seven metabolites were captured and identified by gas chromatography/mass spectrometry (GC–MS) analysis: diazoxon, diazinon aldehyde, isopropenyl derivative of diazinon, hydroxyethyl derivative of diazinon, diazinon methyl ketone, O-[2-(1-hydroxyethyl)-6-methylpyrimidin-4-yl] O-methyl O-hydrogen phosphorothioate, and O-(6-methyl pyrimidin-4-yl) O,O-dihydrogen phosphorothioate. Based on these metabolites, a novel microbial biodegradation pathway of diazinon by Sphingobium sp. DI-6 is proposed. This research provides potentially useful information for the application of the DI-6 strain in bioremediation of diazinon-contaminated environments.
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
mLife
·
2022
·Vol. 1
·期 3
·287-302
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IF 0
Lige Zhang,Huan Liu,Junbiao Dai,Ping Xu,Hongzhi Tang
Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health. The previously isolated phenanthrene-degrading bacterial consortium (PDMC) consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs. To identify the degradation mechanism of PAHs in the consortium PDMC, metagenomic binning was conducted and a Sphingomonadales assembly genome with 100% completeness was obtained. Additionally, Sphingobium sp. SHPJ-2, an efficient degrader of PAHs, was successfully isolated from the consortium PDMC. Strain SHPJ-2 has powerful degrading abilities and various degradation pathways of high-molecular-weight PAHs, including fluoranthene, pyrene, benzo[a]anthracene, and chrysene. Two ring-hydroxylating dioxygenases, five cytochrome P450s, and a pair of electron transfer chains associated with PAH degradation in strain SHPJ-2, which share 83.0%–99.0% similarity with their corresponding homologous proteins, were identified by a combination of Sphingomonadales assembly genome annotation, reverse-transcription quantitative polymerase chain reaction and heterologous expression. Furthermore, when coexpressed in Escherichia coli BL21(DE3) with the appropriate electron transfer chain, PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene, while PhnA2B2 degrade fluoranthene. Altogether, these results provide a comprehensive assessment of strain SHPJ-2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation. Impact statement Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and have attracted widespread attention due to their adverse effects. Several bacteria acquired the capability to degrade PAHs, with Sphingobium strains being the most dominant genus. However, the degradation mechanisms in Sphingobium strains that degrade high-molecular-weight PAHs are poorly understood. Here, Sphingobium sp. strain SHPJ-2, a highly efficient PAH degrader in the phenanthrene-degrading bacterial consortium, was identified and characterized. In addition, several ring-hydroxylating dioxygenases and P450s which can degrade high-molecular-weight PAHs were also identified. Our findings reveal that strain SHPJ-2 has efficient PAHs-degrading genetic resources and could help unveil the degradation mechanisms related to PAH degradation in Sphingomonads.
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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DOI
PLoS One
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2015
·Vol. 10
·期 4
·e0122740
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IF 3.234
Jinxing Hu,Mingrong Qian,Qian Zhang,Jinglan Cui,Chunna Yu,Xiaomei Su,Chaofeng Shen,Muhammad Z. Hashmi,Jiyan Shi
Biphenyl and polychlorinated biphenyls (PCBs) are typical environmental pollutants. However, these pollutants are hard to be totally mineralized by environmental microorganisms. One reason for this is the accumulation of dead-end intermediates during biphenyl and PCBs biodegradation, especially benzoate and chlorobenzoates (CBAs). Until now, only a few microorganisms have been reported to have the ability to completely mineralize biphenyl and PCBs. In this research, a novel bacterium HC3, which could degrade biphenyl and PCBs without dead-end intermediates accumulation, was isolated from PCBs-contaminated soil and identified as Sphingobium fuliginis . Benzoate and 3-chlorobenzoate (3-CBA) transformed from biphenyl and 3-chlorobiphenyl (3-CB) could be rapidly degraded by HC3. This strain has strong degradation ability of biphenyl, lower chlorinated (mono-, di- and tri-) PCBs as well as mono-CBAs, and the biphenyl/PCBs catabolic genes of HC3 are cloned on its plasmid. It could degrade 80.7% of 100 mg L −1 biphenyl within 24 h and its biphenyl degradation ability could be enhanced by adding readily available carbon sources such as tryptone and yeast extract. As far as we know, HC3 is the first reported that can degrade biphenyl and 3-CB without accumulation of benzoate and 3-CBA in the genus Sphingobium , which indicates the bacterium has the potential to totally mineralize biphenyl/PCBs and might be a good candidate for restoring biphenyl/PCBs-polluted environments.
研究领域:
环境微生物学
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污染治理
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产品关联
DOI
PubMed
高影响因子
CURRENT MICROBIOLOGY
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2026
·Vol. 83
·期 4
·207
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IF 2.8
Lu Xie-Feng,Gao Peng,Zhang Shu-Yi,Xu Yuan-Jia,Liu Guo-Hong,Chen Man,Zhou Shun-Gui
Two Gram-stain positive, motile, aerobic, yellowish rod-shaped bacterial strains sgz301303 and sgz301304 T were isolated from the paddy soils. The 16S rRNA gene phylogenetic analysis revealed that both strains belong to the genus Sphingobium , and exhibited the highest sequence similarity (98.3%) with reference strain Sphingobium amiense JCM 11777 T . The draft genome of sgz301304 T has a size of 4.3 Mbp, with DNA G + C content of 64.5%. Whole-genome relatedness analyses showed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain sgz301304 T and S. amiense JCM 11777 T were 82.3% and 25.7%, respectively, both below the accepted species delineation thresholds. The main quinone was Q-10, and the main fatty acids included C 14:0 2-OH (11.3%), and Summed Features 8 (46.6%). Phylogenetic, genomic and phenotypic analyses suggest that strain sgz301304 T belongs to a novel species within the genus of Sphingobium . Therefore, it is recommended to be named as Sphingobium agrisoil sp. nov. The type strain is sgz301304 T (= MCCC 1K09180 T = JCM 37704 T ), respectively.
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DOI
PubMed
高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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2025
·
IF 3.7
Ruomu Chen,Yutian Gan,Wanting Huang,Chenyang Wang,Junhong Ge,Yuanyuan Cheng,Wenjing Qiao,Jiandong Jiang,Kai Chen
Bisphenol F (BPF) is an emerging environmental pollutant widely present in surface water and wastewater systems. Microbial activity is crucial in driving its degradation, offering a potential avenue for mitigating its environmental impact. Although the degradation pathway for BPF has been identified in various bacteria, the biodegradation mechanisms remain unclear. In this study, we isolated a highly efficient BPF-degrading strain of Sphingobium yanoikuyae DN12, which could utilize BPF as the sole carbon and energy source for growth, from a river sediment in Anhui Province, China. Through ultra-performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS) analysis, we found that oxidation and hydrolysis are key steps for BPF biodegradation. Utilizing whole-genome sequencing, comparative transcriptomics analysis, and biochemical identification, a gene cluster bpf was identified to be involved in BPF degradation. BpfAB is a two-component oxidoreductase responsible for converting BPF to 4,4'-dihydroxybenzophenone (DHBP). BpfC is a Baeyer–Villiger monooxygenase responsible for converting DHBP to 4-hydroxyphenyl-4-hydroxybenzoate (HPHB). Isotope tracing demonstrated that the oxygen atom incorporated by BpfAB originates from water, whereas that incorporated by BpfC derives from molecular oxygen (O2). BpfD is an α/β hydrolase responsible for converting HPHB to 4-hydroxybenzoate and 1,4-hydroquinone. Analysis of the taxonomic and habitat of 325 prokaryotic genomes revealed that BpfA-like homologs are predominantly found in the phylum Pseudomonadota, primarily inhabiting soil and aquatic environments. This study enhances our understanding of the biodegradation mechanism of BPF and provides guidance for the effective remediation of BPF-contaminated environments.
研究领域:
环境微生物学
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生物修复
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微生物代谢
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环境科学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
ENVIRONMENTAL SCIENCE & TECHNOLOGY
·
2020
·
IF 7.864
Xiaodan Ma,Bin Liang,Mengyuan Qi,Hui Yun,Ke Shi,Zhiling Li,Yuanqiang Guo,Peisheng Yan,Shuang-Jiang Liu,Aijie Wang
The chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a refractory contaminant that is widely present in various environments. However, few CAP-mineralizing bacteria have been documented, and a complete CAP catabolism pathway has yet to be identified. In this study, the bacterial strain Sphingobium sp. CAP-1 was isolated from an activated sludge sample and was shown to be capable of aerobically subsisting on CAP as the sole carbon, nitrogen, and energy source while simultaneously and efficiently degrading CAP. p-Nitrobenzoic acid (PNBA), p-nitrobenzaldehyde (PNBD), protocatechuate (PCA), and the novel side chain C3-hydroxy-oxygenated product of CAP (O-CAP) were identified during CAP degradation. Strain CAP-1 was able to convert O-CAP to intermediate product PNBA. The putative functional genes associated with PNBA catabolism into the tricarboxylic acid cycle via PCA and floc formation were also identified by genome sequencing and comparative proteome analysis. A complete pathway for CAP catabolism was proposed. The discovery of a novel CAP oxidation/detoxification process and a complete pathway for CAP catabolism enriches the fundamental understanding of the bacterial catabolism of antibiotics, providing new insights into the microbial-mediated fate, transformation, and resistance risk of CAP in the environment. The molecular basis of CAP catabolism and floc formation in strain CAP-1 also offers theoretical guidance for the enhanced bioremediation of CAP-containing environments.
研究领域:
环境微生物学
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生物降解
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基因组学
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抗生素污染
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产品关联
DOI
PubMed
高影响因子
ENVIRONMENTAL SCIENCE & TECHNOLOGY
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2021
·
IF 9.028
Mengyuan Qi,Bin Liang,Long Zhang,Xiaodan Ma,Lei Yan,Wenchen Dong,Deyong Kong,Liying Zhang,Haizhen Zhu,Shu-Hong Gao,Jiandong Jiang,Shuang-Jiang Liu,Philippe F.-X. Corvini,Aijie Wang
Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (−C–S–N– bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.
研究领域:
环境微生物学
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生物修复
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生态学
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微生物生态学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2025
·
IF 11.3
Junxin Zhang,Minghan Zhu,Xiaofang Ouyang,Yibo Yuan,Shaoyu Tang,Hua Yin
Tetrabromobisphenol A (TBBPA), a hydrophobic and persistent brominated flame retardant, has attracted considerable attention due to its potential ecotoxicity. Herein, a newly isolated Sphingobium sp. strain QY1-1 was employed to degrade TBBPA under optimized conditions determined by response surface methodology and kinetic analysis. Complete degradation of TBBPA was achieved by the fourth day under optimal conditions. Five main transformation pathways, i.e., debromination, hydroxylation, O-methylation, sulfation, and glycosylation, were proposed for TBBPA biodegradation based on 19 intermediates including two novel transformation products. The toxicity prediction of TBBPA and its degradation products suggested that the biodegradation of TBBPA by strain QY1-1 could effectively reduce its biotoxicity in aquatic environments. Moreover, transcriptomic analysis revealed significant up-regulation of multiple genes encoding oxidoreductases, lyases, free radical proteins, transporter proteins, and efflux transporters, particularly in the presence of glucose. This indicated that these functional enzymes could be involved in the transmembrane transport and catabolism of TBBPA and its by-products. Additionally, the overexpression of genes encoding chemotactic proteins and antioxidant-defense-related enzymes implied that the addition of glucose could heighten the adaptability of strain QY1-1 to TBBPA stress. This study provides new insights into the biodegradation of TBBPA by Sphingobium sp. and potential strategies for its enhancement.
研究领域:
环境科学
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微生物学
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毒理学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）