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Ruan W, Peng Y, Liao R, Man Y, Tai Y, Tam NFY, Zhang L, Dai Y, Yang Y. Removal, transformation and ecological risk assessment of pesticide in rural wastewater by field-scale horizontal flow constructed wetlands of treated effluent. WATER RESEARCH 2024; 256:121568. [PMID: 38593607 DOI: 10.1016/j.watres.2024.121568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
Constructed wetlands (CWs) are widely used in sewage treatment in rural areas, but there are only a few studies on field-scale CWs in treating wastewater-borne pesticides. In this study, the treatment and metabolic transformation of 29 pesticides in rural domestic sewage by 10 field-scale horizontal flow CWs (HF-CWs), each with a treatment scale of 36‒5000 m3/d and operated for 2‒10 years, in Guangzhou, Southern China was investigated. The risk of pesticides in treated effluent and main factors influencing such risk were evaluated. Results demonstrated that HF-CWs could remove pesticides in sewage and reduce their ecological risk in effluent, but the degree varied among types of pesticides. Herbicides had the highest mean removal rate (67.35 %) followed by insecticides (60.13 %), and the least was fungicides (53.22 %). In terms of single pesticide compounds, the mean removal rate of butachlor was the highest (73.32 %), then acetochlor (69.41 %), atrazine (68.28 %), metolachlor (58.40 %), and oxadixyl (53.28 %). The overall removal rates of targeted pesticides in each HF-CWs ranged from 11 %‒57 %, excluding two HF-CWs showing increases in pesticides in treated effluent. Residues of malathion, phorate, and endosulfan in effluent had high-risks (RQ > 5). The pesticide concentration in effluent was mainly affected by that in influent (P = 0.042), and source control was the key to reducing risk. The main metabolic pathways of pesticide in HF-CWs were oxidation, with hydroxyl group to carbonyl group or to form sulfones, the second pathways by hydrolysis, aerobic condition was conducive to the transformation of pesticides. Sulfones were generally more toxic than the metabolites produced by hydrolytic pathways. The present study provides a reference on pesticides for the purification performance improvement, long-term maintenance, and practical sustainable application of field-scale HF-CWs.
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Affiliation(s)
- Weifeng Ruan
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
| | - Yanqin Peng
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
| | - Ruomei Liao
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
| | - Ying Man
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yiping Tai
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China.
| | - Nora Fung-Yee Tam
- School of Science and Technology, The Hong Kong Metropolitan University, Ho Man Tin, Kowloon 999077, Hong Kong, China
| | - Longzhen Zhang
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Yunv Dai
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
| | - Yang Yang
- Institute of Hydrobiology and Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China.
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Ji J, Pei J, Ding F, Zeng C, Zhou J, Dong W, Cui Z, Yan X. Isolation and characterization of polyester polyurethane-degrading bacterium Bacillus sp. YXP1. ENVIRONMENTAL RESEARCH 2024; 249:118468. [PMID: 38354881 DOI: 10.1016/j.envres.2024.118468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Microorganisms have the potential to be applied for the degradation or depolymerization of polyurethane (PU) and other plastic waste, which have attracted global attention. The appropriate strain or enzyme that can effectively degrade PU is the key to treat PU plastic wastes by biological methods. Here, a polyester PU-degrading bacterium Bacillus sp. YXP1 was isolated and identified from a plastic landfill. Three PU substrates with increasing structure complexities, including Impranil DLN, poly (1,4-butylene adipate)-based PU (PBA-PU), and polyester PU foam, were used to evaluate the degradation capacity of Bacillus sp. YXP1. Under optimal conditions, strain YXP1 could completely degrade 0.5% Impranil DLN within 7 days. After 30 days, the weight loss of polyester PU foam by strain YXP1 was as high as 42.1%. In addition, PBA-PU was applied for degradation pathway analysis due to its clear composition and chemical structure. Five degradation intermediates of PBA-PU were identified, including 4,4'-methylenedianiline (MDA), 1,4-butanediol, adipic acid, and two MDA derivates, indicating that strain YXP1 could depolymerize PBA-PU by the hydrolysis of ester and urethane bonds. Furthermore, the extracellular enzymes produced by strain YXP1 could hydrolyze PBA-PU to generate MDA. Together, this study provides a potential bacterium for the biological treatment of PU plastic wastes and for the mining of functional enzymes.
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Affiliation(s)
- Junbin Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Nanjing Key Laboratory of Quality and Safety of Agricultural Products, College of Food Science, Nanjing XiaoZhuang University, Nanjing, Jiangsu 211171, China
| | - Jing Pei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Fanghui Ding
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Caiting Zeng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jie Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Weiliang Dong
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Chen X, Zhang Y, Liu J. A novel enrofloxacin-degrading fungus, Humicola sp. KC0924g, isolated from the rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L. Int Microbiol 2024:10.1007/s10123-024-00513-x. [PMID: 38506947 DOI: 10.1007/s10123-024-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/01/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
A novel enrofloxacin-degrading fungus was isolated from a rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L.. The isolate, designated KC0924g, was identified as a member of the genus Humicola based on morphological characteristics and tandem conserved sequence analysis. The optimal temperature and pH for enrofloxacin degradation by strain KC0924g were 28 °C and 9.0, respectively. Under such condition, 98.2% of enrofloxacin with an initial concentration of 1 mg L-1 was degraded after 72 h of incubation, with nine possible degradation products identified. Four different metabolic pathways were proposed, which were initiated by cleavage of the piperazine moiety, hydroxylation of the aromatic ring, oxidative decarboxylation, or defluorination. In addition to enrofloxacin, strain KC0924g also degraded other fluoroquinolone antibiotics (ciprofloxacin, norfloxacin, and ofloxacin), malachite green (an illegal additive in aquaculture), and leucomalachite green. Pretreatment of cells of strain KC0924g with Cu2+ accelerated ENR degradation. Furthermore, it was speculated that a flavin-dependent monooxygenase was involved in ENR degradation, based on the increased transcriptional levels of these two genes after Cu2+ induction. This work enriches strain resources for enrofloxacin remediation and, more importantly, would facilitate studies on the molecular mechanism of ENR degradation with degradation-related transcriptome available.
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Affiliation(s)
- Xueting Chen
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, No.265 Jiamusi Road, Yangpu District, Shanghai, 200433, China.
| | - Yuping Zhang
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, No.265 Jiamusi Road, Yangpu District, Shanghai, 200433, China
| | - Jinghua Liu
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, No.265 Jiamusi Road, Yangpu District, Shanghai, 200433, China
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Zeng B, Zhang F, Liu YT, Wu SF, Bass C, Gao CF. Symbiotic bacteria confer insecticide resistance by metabolizing buprofezin in the brown planthopper, Nilaparvata lugens (Stål). PLoS Pathog 2023; 19:e1011828. [PMID: 38091367 PMCID: PMC10718449 DOI: 10.1371/journal.ppat.1011828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Buprofezin, a chitin synthesis inhibitor, is widely used to control several economically important insect crop pests. However, the overuse of buprofezin has led to the evolution of resistance and exposed off-target organisms present in agri-environments to this compound. As many as six different strains of bacteria isolated from these environments have been shown to degrade buprofezin. However, whether insects can acquire these buprofezin-degrading bacteria from soil and enhance their own resistance to buprofezin remains unknown. Here we show that field strains of the brown planthopper, Nilaparvata lugens, have acquired a symbiotic bacteria, occurring naturally in soil and water, that provides them with resistance to buprofezin. We isolated a symbiotic bacterium, Serratia marcescens (Bup_Serratia), from buprofezin-resistant N. lugens and showed it has the capacity to degrade buprofezin. Buprofezin-susceptible N. lugens inoculated with Bup_Serratia became resistant to buprofezin, while antibiotic-treated N. lugens became susceptible to this insecticide, confirming the important role of Bup_Serratia in resistance. Sequencing of the Bup_Serratia genome identified a suite of candidate genes involved in the degradation of buprofezin, that were upregulated upon exposure to buprofezin. Our findings demonstrate that S. marcescens, an opportunistic pathogen of humans, can metabolize the insecticide buprofezin and form a mutualistic relationship with N. lugens to enhance host resistance to buprofezin. These results provide new insight into the mechanisms underlying insecticide resistance and the interactions between bacteria, insects and insecticides in the environment. From an applied perspective they also have implications for the control of highly damaging crop pests.
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Affiliation(s)
- Bin Zeng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, People’s Republic of China
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, United Kingdom
| | - Fan Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, People’s Republic of China
| | - Ya-Ting Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, People’s Republic of China
| | - Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, People’s Republic of China
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, United Kingdom
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, People’s Republic of China
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Ma Q, Meng N, Su J, Li Y, Gu J, Wang Y, Wang J, Qu Y, Zhao Z, Sun Y. Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies. J Environ Sci (China) 2023; 127:688-699. [PMID: 36522097 DOI: 10.1016/j.jes.2022.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 06/17/2023]
Abstract
3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiazheng Gu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yidi Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid. Appl Environ Microbiol 2022; 88:e0036022. [PMID: 35766505 PMCID: PMC9317849 DOI: 10.1128/aem.00360-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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Characterization of the 2,6-Dimethylphenol Monooxygenase MpdAB and Evaluation of Its Potential in Vitamin E Precursor Synthesis. Appl Environ Microbiol 2022; 88:e0011022. [PMID: 35380460 DOI: 10.1128/aem.00110-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,6-Dimethylphenol (2,6-DMP) is a widely used chemical intermediate whose residue has been frequently detected in the environment, posing a threat to some aquatic organisms. Microbial degradation is an effective method to eliminate 2,6-DMP in nature. However, the genetic and biochemical mechanisms of 2,6-DMP metabolism remain unknown. Mycobacterium neoaurum B5-4 is a 2,6-DMP-degrading bacterium isolated in our previous study. Here, a 2,6-DMP degradation-deficient mutant of strain B5-4 was screened. Comparative genomic, transcriptomic, gene disruption, and genetic complementation data indicated that mpdA and mpdB are responsible for the initial step of 2,6-DMP degradation in M. neoaurum B5-4. MpdAB was predicted to be a two-component flavin-dependent monooxygenase system, which shows 32% and 36% identities with HsaAB from Mycobacterium tuberculosis CDC1551. The transcription of mpdA and mpdB was substantially increased upon exposure to 2,6-DMP. Nuclear magnetic resonance analysis showed that purified 6×His-MpdA and 6×His-MpdB hydroxylated 2,6-DMP and 2,3,6-trimethylphenol (2,3,6-TMP) at the para-position using NADH and flavin adenine dinucleotide (FAD) as cofactors. The apparent Km values of MpdAB for 2,6-DMP and 2,3,6-TMP were 0.12 ± 0.01 and 0.17 ± 0.01 mM, respectively, and the corresponding kcat/Km values were 4.02 and 2.84 s-1 mM-1, respectively. Since para-hydroxylated 2,3,6-TMP is a major precursor for vitamin E synthesis, the potential of MpdAB in vitamin E synthesis was preliminarily evaluated using whole-cell catalysis. Low expression levels of MpdA and 2,3,6-TMP cytotoxicity limited the efficiency of whole-cell catalysis. Together, this study reveals the genetic and biochemical basis for the initial step of 2,6-DMP biodegradation and provides candidate enzymes for vitamin E synthesis. IMPORTANCE Although the microbial degradation of the six isomers of dimethylphenol has been extensively studied, the genetic and biochemical mechanisms of 2,6-DMP degradation remain unclear. This study identified the genes responsible for the initial step in the 2,6-DMP catabolic pathway in M. neoaurum B5-4. Moreover, MpdAB also catalyzed the transformation of 2,3,6-TMP to 2,3,5-trimethylhydroquinone (2,3,5-TMHQ), a crucial step in vitamin E synthesis. Overall, this study provides candidate enzymes for both the bioremediation of 2,6-DMP contamination and the development of a green method to synthesize vitamin E.
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Cheng M, Qian Y, Xing Z, Zylstra GJ, Huang X. The low-nanomolar 4-nitrobenzoate-responsive repressor PnbX negatively regulates the actinomycete-derived 4-nitrobenzoate-degrading pnb locus. Environ Microbiol 2021; 23:7028-7041. [PMID: 34554625 DOI: 10.1111/1462-2920.15787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
Nitroaromatic compounds pose severe threats to public health and environmental safety. Nitro group removal via ammonia release is an important strategy for bacterial detoxification of nitroaromatic compounds, such as the conversion of 4-nitrobenzoate (4-NBA) to protocatechuate by the bacterial pnb operon. In contrast to the LysR-family transcriptional regulator PnbR in proteobacteria, the actinomycete-derived pnb locus (4-NBA degradation structural genes) formed an operon with the TetR-family transcriptional regulator gene pnbX, implying that it has a distinct regulatory mechanism. Here, pnbBA from the actinomycete Nocardioides sp. strain LMS-CY was biochemically confirmed to express 4-NBA degradation enzymes, and pnbX was essential for inducible degradation of 4-NBA. Purified PnbX-6His could bind the promoter probe of the pnb locus in vitro, and 4-NBA prevented this binding. 4-NBA could bind PnbX at a 1:1 molar ratio with KD = 26.7 ± 4.2 nM. Low-nanomolar levels of 4-NBA induced the transcription of the pnb operon in strain LMS-CY. PnbX bound a palindromic sequence motif (5'-TTACGTTACA-N8 -TGTAACGTAA-3') that encompasses the pnb promoter. This study identified a TetR-family repressor for the actinomycete-derived pnb operon that recognizes 10-8 M 4-NBA as its ligand, implying that nitro group removal of nitroaromatic compounds may be especially important for actinomycetes.
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Affiliation(s)
- Minggen Cheng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yingying Qian
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ziyu Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Gerben J Zylstra
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Xing Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Huang H, Liu Z, Qiu Y, Wang X, Wang H, Xiao H, Lu Z. Efficient electrotransformation of Rhodococcus ruber YYL with abundant extracellular polymeric substances via a cell wall-weakening strategy. FEMS Microbiol Lett 2021; 368:6273628. [PMID: 33974050 DOI: 10.1093/femsle/fnab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/08/2021] [Indexed: 11/14/2022] Open
Abstract
Rhodococcus spp. have broad potential applications related to the degradation of organic contaminants and the transformation or synthesis of useful compounds. However, some Gram-positive bacteria are difficult to manipulate genetically due to low transformation efficiency. In this study, we investigated the effects of chemicals including glycine, isonicotinic acid hydrazide (INH), Tween 80 and penicillin G, as well as cell growth status, competent cell concentration, electroporation field strength, electroporation time and heat shock time, on the electrotransformation efficiency of the tetrahydrofuran-degrading bacterium Rhodococcus ruber YYL with low transformation efficiency. The highest electrotransformation efficiency was 1.60 × 106 CFU/µg DNA after parameter optimization. GmhD (D-glycero-D-manno-heptose 1-phosphate guanosyltransferase) gene, which is important in the biosynthesis of lipopolysaccharide, was deleted via the optimized electrotransformation method. Compared with wild-type strain, YYL ΔgmhD showed extremely high electrotransformation efficiency because the surface of it had no mushroom-like extracellular polymeric substances (EPS). In addition, the results showed that cell wall-weakening reagents might cause some translucent substances like EPS, to detach from the cells, increasing the electrotransformation efficiency of strain YYL. We propose that these results could provide a new strategy for unique bacteria that are rich in EPS, for which genetic manipulation systems are difficult to establish.
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Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zubi Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yiyang Qiu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hailong Xiao
- Hangzhou Institute for Food and Drug Control, Hangzhou, Zhejiang 310018, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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11
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Mu Y, Chen Q, Parales RE, Lu Z, Hong Q, He J, Qiu J, Jiang J. Bacterial catabolism of nicotine: Catabolic strains, pathways and modules. ENVIRONMENTAL RESEARCH 2020; 183:109258. [PMID: 32311908 DOI: 10.1016/j.envres.2020.109258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/22/2020] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
Nicotine, the major alkaloid in tobacco, is a toxic, carcinogenic, and addictive compound. In recent years, nicotine catabolism in prokaryotes, including the catabolic pathways for its degradation and the catabolic genes that encode the enzymes of these pathways, have been systemically investigated. In this review, the three known pathways for nicotine catabolism in bacteria are summarized: the pyridine pathway, the pyrrolidine pathway, and a variation of the pyridine and pyrrolidine pathway (VPP pathway). The three nicotine catabolic pathways appear to have evolved separately in three distantly related lineages of bacteria. However, the general mechanism for the breakdown of the nicotine molecule in all three pathways is conserved and can be divided into six major enzymatic steps or catabolic modules that involve hydroxylation of the pyridine ring, dehydrogenation of the pyrrolidine ring, cleavage of the side chain, cleavage of the pyridine ring, dehydrogenation of the side chain, and deamination of pyridine ring-lysis products. In addition to summarizing our current understanding of nicotine degradation pathways, we identified several potential nicotine-degrading bacteria whose genome sequences are in public databases by comparing the sequences of conserved catabolic enzymes. Finally, several uncharacterized genes that are colocalized with nicotine degradation genes and are likely to be involved in nicotine catabolism, including regulatory genes, methyl-accepting chemotaxis protein genes, transporter genes, and cofactor genes are discussed. This review provides a comprehensive overview of the catabolism of nicotine in prokaryotes and highlights aspects of the process that still require additional research.
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Affiliation(s)
- Yang Mu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China; Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Zhenmei Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qing Hong
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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12
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Wang H, Liu X, Wu C, Zhang M, Ke Z, Jiang W, Zhou Y, Qiu J, Hong Q. An angular dioxygenase gene cluster responsible for the initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp. WH99 can protect sensitive organisms from toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135726. [PMID: 31837849 DOI: 10.1016/j.scitotenv.2019.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
A bacterial strain, Rhodococcus sp. WH99, capable of degrading phenazine-1-carboxylic acid (PCA) was isolated and characterized. Genome comparison revealed that a 21499-bp DNA fragment containing a putative angular dioxygenase gene cluster consisting of the dioxygenase-, ferredoxin reductase- and ferredoxin-encoding genes (pzcA1A2, pzcC and pzcD) is missed in the PCA degradation-deficient mutant WH99M. The pzcA1A2CD genes were expressed in Escherichia coli respectively and hydroxylation of PCA to 1,2-dihydroxyphenazine occurred in vitro only when all components were present. However, in vivo analyses showed that pzcA1A2 and pzcD were indispensable for PCA degradation, while PzcC can be partially replaced by other ferredoxin reductases. Hydroxylation of PCA not only initiates degradation of PCA in strain WH99 but also provides protection to sensitive organisms that would otherwise be inhibited by PCA toxicity. This study illustrates a new initial PCA degradation step in Gram-positive bacteria and enhances our understanding of the genes responsible for PCA hydroxylation, thus enabling targeted studies on protection by PCA degradation in diverse environments.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Xiaoan Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China.
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13
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Ji J, Zhang Y, Liu Y, Zhu P, Yan X. Biodegradation of plastic monomer 2,6-dimethylphenol by Mycobacterium neoaurum B5-4. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113793. [PMID: 31864921 DOI: 10.1016/j.envpol.2019.113793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/06/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
2,6-Dimethylphenol (2,6-DMP), an important chemical intermediate and the monomer of plastic polyphenylene oxide, is widely used in chemical and plastics industry. However, the pollution problem of 2,6-DMP residues is becoming increasingly serious, which is harmful to some aquatic animals. Microbial degradation provided an effective approach to eliminate DMPs in nature, which is considered as a prospective way to remediate DMPs-contaminated environments. But the 2,6-DMP-degrading bacteria is not available and the molecular mechanism of 2,6-DMP degradation is unclear as well. Here, a 2,6-DMP-degrading bacterium named B5-4 was isolated and identified as Mycobacterium neoaurum. M. neoaurum B5-4 could utilize 2,6-DMP as the sole carbon source for growth. Furthermore, M. neoaurum B5-4 could degrade 2,6-DMP with concentrations ranging from 1 to 500 mg L-1. Six intermediate metabolites of 2,6-DMP were identified and a metabolic pathway of 2,6-DMP in M. neoaurum B5-4 was proposed, in which 2,6-DMP was initially converted to 2,6-dimethyl-hydroquinone and 2,6-dimethyl-3-hydroxy-hydroquinone by two consecutive hydroxylations at C-4 and γ position; 2,6-dimethyl-3-hydroxy-hydroquinone was then subjected to aromatic ring ortho-cleavage to produce 2,4-dimethyl-3-hydroxymuconic acid, which was further transformed to citraconate, and subsequently into TCA cycle. In addition, toxicity bioassay of 2,6-DMP in water using zebrafish indicates that 2,6-DMP is toxic to zebrafish and M. neoaurum B5-4 could effectively eliminate 2,6-DMP in water to protect zebrafish from 2,6-DMP-induced death. This work provides a potential strain for bioremediation of 2,6-DMP-contaminated environments and lays a foundation for elucidating the molecular mechanism and genetic determinants of 2,6-DMP degradation.
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Affiliation(s)
- Junbin Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Yanting Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Yongchuang Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Pingping Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China; Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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Huang J, Chen D, Cheng X, Liu G, Wang G, Jiang J. Enantioselective Catabolism of Napropamide Chiral Enantiomers in Sphingobium sp. A1 and B2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6819-6827. [PMID: 31135148 DOI: 10.1021/acs.jafc.9b00707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Napropamide [ N, N-diethyl-2-(1-naphthalenyloxy)propenamide, NAP] is a highly efficient and broad-spectrum amide herbicide. Little is known about the bacterial catabolism of its different enantiomers. Here, we report the isolation of two NAP-degrading strains of Sphingobium sp., A1 and B2, and the different catabolic pathways of different enantiomers in these two strains. Strain A1 dioxygenated NAP at different positions of the naphthalene ring of different enantiomers, leading to the complete degradation of R-NAP while producing a dead-end product from S-NAP. Strain B2 cleaved the amido bonds of both enantiomers, but only the product from S-NAP could be further transformed to form α-naphthol and mineralize in strain B2. The degradation rates of R-NAP and S-NAP in the combination degradation by strains A1 and B2 were 24.8 and 7.5 times that in the single-strain degradation by strain B2 or A1, respectively, showing enhanced synergistic catabolism between strains A1 and B2. This study provides new insights into the enantioselective catabolic network of the chiral herbicide NAP in microorganisms.
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Affiliation(s)
| | | | | | | | | | - Jiandong Jiang
- Jiangsu Key Lab for Solid Organic Waste Utilization , Nanjing , Jiangsu 210095 , People's Republic of China
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