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Huang Q, Liu Z, Guo Y, Li B, Yang Z, Liu X, Ni J, Li X, Zhang X, Zhou N, Yin H, Jiang C, Hao L. Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162330. [PMID: 36813198 DOI: 10.1016/j.scitotenv.2023.162330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhenghua Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, PR China
| | - Yuan Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Bao Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhenni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaoling Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Jianmei Ni
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, PR China.
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2
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Palomino A, Gewurz D, DeVine L, Zajmi U, Moralez J, Abu-Rumman F, Smith RP, Lopatkin AJ. Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment. THE ISME JOURNAL 2023; 17:151-162. [PMID: 36261510 PMCID: PMC9750983 DOI: 10.1038/s41396-022-01329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 12/15/2022]
Abstract
Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.
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Affiliation(s)
- Alana Palomino
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Danya Gewurz
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Lela DeVine
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Ujana Zajmi
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Jenifer Moralez
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Fatima Abu-Rumman
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Robert P. Smith
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA ,grid.261241.20000 0001 2168 8324Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Allison J. Lopatkin
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Data Science Institute, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Systems Biology, Columbia University, New York, NY 10027 USA ,grid.16416.340000 0004 1936 9174Department of Chemical Engineering, University of Rochester, Rochester, NY 14627 USA
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Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux. Appl Environ Microbiol 2022; 88:e0118222. [PMID: 36036586 PMCID: PMC9499029 DOI: 10.1128/aem.01182-22] [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
Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N11-ATG), compared to those of odcA/orf419 (CAT-N11-ATG) and odcC (CAT-N11-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.
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Chen K, Xu X, Yang M, Liu T, Liu B, Zhu J, Wang B, Jiang J. Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats. Environ Microbiol 2022; 24:5123-5138. [PMID: 35876302 DOI: 10.1111/1462-2920.16141] [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: 04/04/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Muji Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tairong Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Bin Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jianchun Zhu
- Laboratory Centre of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
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5
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Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nat Ecol Evol 2021; 5:431-441. [PMID: 33526890 DOI: 10.1038/s41559-020-01385-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/11/2020] [Indexed: 01/30/2023]
Abstract
Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent advances in ecological coexistence theory offer a powerful framework to probe the mechanisms regulating intra- and interspecific competition, but the significance of this body of theory to the problem of antibiotic resistance has been largely overlooked. In this Perspective, we draw on emerging ecological theory to illustrate how changes in resource niche overlap can be equally important as changes in competitive ability for understanding costs of resistance and the persistence of resistant pathogens in microbial communities. We then show how different temporal patterns of resource and antibiotic supply, alongside trade-offs in competitive ability at high and low resource concentrations, can have diametrically opposing consequences for the coexistence and exclusion of resistant and susceptible strains. These insights highlight numerous opportunities for innovative experimental and theoretical research into the ecological dimensions of antibiotic resistance.
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6
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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7
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Whittington HD, Singh M, Ta C, Azcárate-Peril MA, Bruno-Bárcena JM. Accelerated Biodegradation of the Agrochemical Ametoctradin by Soil-Derived Microbial Consortia. Front Microbiol 2020; 11:1898. [PMID: 32982997 PMCID: PMC7477900 DOI: 10.3389/fmicb.2020.01898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023] Open
Abstract
Pesticide-resistant plant pathogens are an increasing threat to the global food supply and have generated a need for novel, efficacious agrochemicals. The current regulatory process for approving new agrochemicals is a tedious but necessary process. One way to accelerate the safety evaluation process is to utilize in vitro systems to demonstrate pesticide degradation by soil microbes prior to ex vivo soil evaluations. This approach may have the capability to generate metabolic profiles free of inhibitory substances, such as humic acids, commonly present in ex vivo soil systems. In this study, we used a packed-bed microbial bioreactor to assess the role of the natural soil microbial community during biodegradation of the triazolopyrimidine fungicide, ametoctradin. Metabolite profiles produced during in vitro ametoctradin degradation were similar to the metabolite profiles obtained during environmental fate studies and demonstrated the degradation of 81% of the parent compound in 72 h compared to a half-life of 2 weeks when ametoctradin was left in the soil. The microbial communities of four different soil locations and the bioreactor microbiome were compared using high throughput sequencing. It was found that biodegradation of ametoctradin in both ex vivo soils and in vitro in the bioreactor correlated with an increase in the relative abundance of Burkholderiales, well characterized microbial degraders of xenobiotic compounds.
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Affiliation(s)
- Hunter D Whittington
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Mahatam Singh
- BASF Corporation, Research Triangle Park, NC, United States
| | - Chanh Ta
- BASF Corporation, Research Triangle Park, NC, United States
| | - M Andrea Azcárate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - José M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Storck V, Gallego S, Vasileiadis S, Hussain S, Béguet J, Rouard N, Baguelin C, Perruchon C, Devers-Lamrani M, Karpouzas DG, Martin-Laurent F. Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes ( pdmAB) in a Biobed System. Appl Environ Microbiol 2020; 86:e00474-20. [PMID: 32414799 PMCID: PMC7357488 DOI: 10.1128/aem.00474-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/30/2020] [Indexed: 01/10/2023] Open
Abstract
Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.
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Affiliation(s)
- Veronika Storck
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sara Gallego
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Sabir Hussain
- Department of Environmental Sciences and Engineering, Government College, University of Faisalabad, Faisalabad, Pakistan
| | - Jérémie Béguet
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Céline Baguelin
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
- Hydreka Enoveo, Lyon, France
| | - Chiara Perruchon
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Marion Devers-Lamrani
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Fabrice Martin-Laurent
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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9
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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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10
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Werner J, Nour E, Bunk B, Spröer C, Smalla K, Springael D, Öztürk B. PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera. Front Microbiol 2020; 11:149. [PMID: 32132980 PMCID: PMC7039861 DOI: 10.3389/fmicb.2020.00149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/22/2020] [Indexed: 01/31/2023] Open
Abstract
PromA plasmids are broad host range (BHR) plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two of which originated from unrelated Hydrogenophaga hosts isolated from different environments (pPBL-H3-2 and pBPS33-2), and one (pEN1) which was exogenously captured from an on-farm biopurification system (BPS). Hydrogenophaga sp. plasmid pBPS33-2 carries all three necessary gene clusters (hylA, dca, ccd) determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Hydrogenophaga sp. plasmid pPBL-H3-2 exists as two variants, both containing ccd but with the hylA and dca gene modules interchanged between each other at exactly the same location. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.
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Affiliation(s)
- Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Eman Nour
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- Faculty of Organic Agriculture, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Boyke Bunk
- Bioinformatics Department, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Central Services, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Başak Öztürk
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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11
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Wang X, Zhao L, Zhang L, Wu Y, Chou M, Wei G. Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution. Lett Appl Microbiol 2018; 67:22-31. [PMID: 29696668 DOI: 10.1111/lam.12998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 11/27/2022]
Abstract
Rhizobial symbiotic plasmids play vital roles in mutualistic symbiosis with legume plants by executing the functions of nodulation and nitrogen fixation. To explore the gene composition and genetic constitution of rhizobial symbiotic plasmids, comparison analyses of 24 rhizobial symbiotic plasmids derived from four rhizobial genera was carried out. Results illustrated that rhizobial symbiotic plasmids had higher proportion of functional genes participating in amino acid transport and metabolism, replication; recombination and repair; carbohydrate transport and metabolism; energy production and conversion and transcription. Mesorhizobium amorphae CCNWGS0123 symbiotic plasmid - pM0123d had similar gene composition with pR899b and pSNGR234a. All symbiotic plasmids shared 13 orthologous genes, including five nod and eight nif/fix genes which participate in the rhizobia-legume symbiosis process. These plasmids contained nod genes from four ancestors and fix genes from six ancestors. The ancestral type of pM0123d nod genes was similar with that of Rhizobium etli plasmids, while the ancestral type of pM0123d fix genes was same as that of pM7653Rb. The phylogenetic trees constructed based on nodCIJ and fixABC displayed different topological structures mainly due to nodCIJ and fixABC ancestral type discordance. The study presents valuable insights into mosaic structures and the evolution of rhizobial symbiotic plasmids. SIGNIFICANCE AND IMPACT OF THE STUDY This study compared 24 rhizobial symbiotic plasmids that included four genera and 11 species, illuminating the functional gene composition and symbiosis gene ancestor types of symbiotic plasmids from higher taxonomy. It provides valuable insights into mosaic structures and the evolution of symbiotic plasmids.
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Affiliation(s)
- X Wang
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - L Zhao
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - L Zhang
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Y Wu
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - M Chou
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - G Wei
- State Key Laboratory of Crop Stress of Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
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Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway. Appl Environ Microbiol 2018; 84:AEM.02467-17. [PMID: 29305508 DOI: 10.1128/aem.02467-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023] Open
Abstract
The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.
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Huang X, He J, Yan X, Hong Q, Chen K, He Q, Zhang L, Liu X, Chuang S, Li S, Jiang J. Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 143:272-297. [PMID: 29183604 DOI: 10.1016/j.pestbp.2016.11.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 06/07/2023]
Abstract
Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.
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Affiliation(s)
- Xing Huang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Qing Hong
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Qin He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Long Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Shaochuang Chuang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Shunpeng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China.
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14
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Li A, Qiu J, Chen D, Ye J, Wang Y, Tong L, Jiang J, Chen J. Characterization and Genome Analysis of a Nicotine and Nicotinic Acid-Degrading Strain Pseudomonas putida JQ581 Isolated from Marine. Mar Drugs 2017; 15:md15060156. [PMID: 28561771 PMCID: PMC5484106 DOI: 10.3390/md15060156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/10/2017] [Accepted: 05/25/2017] [Indexed: 11/17/2022] Open
Abstract
The presence of nicotine and nicotinic acid (NA) in the marine environment has caused great harm to human health and the natural environment. Therefore, there is an urgent need to use efficient and economical methods to remove such pollutants from the environment. In this study, a nicotine and NA-degrading bacterium—strain JQ581—was isolated from sediment from the East China Sea and identified as a member of Pseudomonas putida based on morphology, physio-biochemical characteristics, and 16S rDNA gene analysis. The relationship between growth and nicotine/NA degradation suggested that strain JQ581 was a good candidate for applications in the bioaugmentation treatment of nicotine/NA contamination. The degradation intermediates of nicotine are pseudooxynicotine (PN) and 3-succinoyl-pyridine (SP) based on UV, high performance liquid chromatography, and liquid chromatography-mass spectrometry analyses. However, 6-hydroxy-3-succinoyl-pyridine (HSP) was not detected. NA degradation intermediates were identified as 6-hydroxynicotinic acid (6HNA). The whole genome of strain JQ581 was sequenced and analyzed. Genome sequence analysis revealed that strain JQ581 contained the gene clusters for nicotine and NA degradation. This is the first report where a marine-derived Pseudomonas strain had the ability to degrade nicotine and NA simultaneously.
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Affiliation(s)
- Aiwen Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Jiguo Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dongzhi Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Jiexu Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yuhong Wang
- Nanjing Yuanheng Institute for Environmental Studies Co., Ltd., Nanjing 210049, China.
| | - Lu Tong
- Nanjing Yuanheng Institute for Environmental Studies Co., Ltd., Nanjing 210049, China.
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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