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Wen T, Xie P, Liu H, Liu T, Zhao M, Yang S, Niu G, Hale L, Singh BK, Kowalchuk GA, Shen Q, Yuan J. Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease. Nat Commun 2023; 14:4497. [PMID: 37495619 PMCID: PMC10372070 DOI: 10.1038/s41467-023-40184-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g-1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.
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Affiliation(s)
- Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Green Intelligent Fertilizer Innovation, MARD, Sinong Bio-organic Fertilizer Institute, Nanjing, 210000, China
| | - Penghao Xie
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
| | - Ting Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengdie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guoqing Niu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lauren Hale
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China.
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Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil. mSystems 2022; 7:e0016922. [PMID: 35913191 PMCID: PMC9426591 DOI: 10.1128/msystems.00169-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extensive use of agrochemicals is emerging as a serious environmental issue coming at the cost of the pollution of soil and water resources. Bioremediation techniques such as biostimulation are promising strategies used to remove pollutants from agricultural soils by supporting the indigenous microbial degraders. Though considered cost-effective and eco-friendly, the success rate of these strategies typically varies, and consequently, they are rarely integrated into commercial agricultural practices. In the current study, we applied metabolic-based community-modeling approaches for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Efficacy of biostimulants as enhancers of the indigenous degrader Paenarthrobacter was ranked through simulation and validated in pot experiments. A two-dimensional simulation matrix predicting the effect of different biostimulants on additional potential indigenous degraders (Pseudomonas, Clostridium, and Geobacter) was crossed with experimental observations. The overall ability of the models to predict the compounds that act as taxa-selective stimulants indicates that computational algorithms can guide the manipulation of the soil microbiome in situ and provides an additional step toward the educated design of biostimulation strategies. IMPORTANCE Providing the food requirements of a growing population comes at the cost of intensive use of agrochemicals, including pesticides. Native microbial soil communities are considered key players in the degradation of such exogenous substances. Manipulating microbial activity toward an optimized outcome in efficient biodegradation processes conveys a promise of maintaining intensive yet sustainable agriculture. Efficient strategies for harnessing the native microbiome require the development of approaches for processing big genomic data. Here, we pursued metabolic modeling for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Our genomic-based predictions point at strategies for optimizing biodegradation by the native community. Developing a systematic, data-guided understanding of metabolite-driven targeted enhancement of selected microorganisms lays the foundation for the design of ecologically sound methods for optimizing microbiome functioning.
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Aksu D, Diallo MM, Şahar U, Uyaniker TA, Ozdemir G. High expression of ring-hydroxylating dioxygenase genes ensure efficient degradation of p-toluate, phthalate, and terephthalate by Comamonas testosteroni strain 3a2. Arch Microbiol 2021; 203:4101-4112. [PMID: 34057546 DOI: 10.1007/s00203-021-02395-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Para-toluic acid, a major pollutant in industrial wastewater, is hazardous to human health. It has been demonstrated that Gram-negative bacteria are among the most effective degraders of para-toluic acid. In this study, the ability of Comamonas testosteroni strain 3a2, isolated from a petrochemical industry wastewater, to degrade para-toluic acid was investigated. The effect of different carbon (glucose and ethylene glycol) and nitrogen sources (urea, yeast extract, peptone, NaNO3, NH4NO3) on the biodegradation of para-toluic acid by the isolate 3a2 was evaluated. Furthermore, ring hydroxylating dioxygenase genes were amplified by PCR and their expression was evaluated during the biodegradation of para-toluic acid. The results indicated that strain 3a2 was able to degrade up to 1000 mg/L of para-toluic acid after 14 h. The highest degradation yield was recorded in the presence of yeast extract as nitrogen source. However, the formation of terephthalic acid and phthalic acid was noted during para-toluic acid degradation by the isolate 3a2. Toluate 1,2-dioxygenase, terephthalate 1,2 dioxygenase, and phthalate 4,5 dioxygenase genes were detected in the genomic DNA of 3a2. The induction of ring hydroxylating dioxygenase genes was proportional to the concentration of each hydrocarbon. This study showed that the isolate 3a2 can produce terephthalate and phthalate during the para-toluic acid biodegradation, which were also degraded after 24 h.
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Affiliation(s)
- Didem Aksu
- Application and Research Center for Testing and Analysis, Ege University, Izmir, Turkey.
| | | | - Umut Şahar
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
| | | | - Guven Ozdemir
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
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Esquirol L, Peat TS, Sugrue E, Balotra S, Rottet S, Warden AC, Wilding M, Hartley CJ, Jackson CJ, Newman J, Scott C. Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application. Adv Microb Physiol 2020; 76:129-186. [PMID: 32408946 DOI: 10.1016/bs.ampbs.2020.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.
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Affiliation(s)
- Lygie Esquirol
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Elena Sugrue
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sahil Balotra
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Sarah Rottet
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Andrew C Warden
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia; CSIRO Biomedical Manufacturing, Parkville, VIC, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Carol J Hartley
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Colin Scott
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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Varjani S, Kumar G, Rene ER. Developments in biochar application for pesticide remediation: Current knowledge and future research directions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:505-513. [PMID: 30502618 DOI: 10.1016/j.jenvman.2018.11.043] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
The indiscriminate use of pesticides due to modern agricultural practices has received special attention from the scientific community to address the persistence, recalcitrance and multi-faceted toxicity of several pesticides. Pesticides are hazardous/toxic and can accumulate easily into non-target organisms including humans and other life forms. Several studies have been performed to investigate the effect of biochar addition for pesticide remediation. This review provides a comprehensive information on biochar amendment for the remediation of persistent organic pollutants such as pesticides. The types of pesticides and their hazards to life forms are briefly introduced before detailing biochar production, its characteristics and applications. Biochar addition in pesticide polluted environment offers the following advantages: (a) increases the soil water holding capacity, (b) improves aeration conditions in soil, and (c) provides habitat for the growth of microorganisms, thereby facilitating microbial community for metabolic activities and pesticide degradation. This paper also provides an up-to-date review on remediation of pesticides using biochar, the knowledge gaps and the future research directions in this field to evaluate the effect of biochar addition on agricultural and environmental performances.
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Affiliation(s)
- Sunita Varjani
- Gujarat Pollution Control Board, Sector-10A, Gandhinagar 382010, Gujarat, India.
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus, 4036 Stavanger, Norway
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology, IHE - Delft, Institute of Water Education 2601 DA, Delft, the Netherlands
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6
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Liu X, Chen K, Chuang S, Xu X, Jiang J. Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies. Front Microbiol 2019; 10:88. [PMID: 30761118 PMCID: PMC6363660 DOI: 10.3389/fmicb.2019.00088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/16/2019] [Indexed: 02/01/2023] Open
Abstract
Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.
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Affiliation(s)
| | | | | | - Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Rangasamy K, Athiappan M, Devarajan N, Parray JA, Shameem N, Aruljothi KN, Hashem A, Alqarawi AA, Abd_Allah EF. Cloning and Expression of the Organophosphate Pesticide-Degrading α- β Hydrolase Gene in Plasmid pMK-07 to Confer Cross-Resistance to Antibiotics. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1535209. [PMID: 29862253 PMCID: PMC5976953 DOI: 10.1155/2018/1535209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/08/2018] [Indexed: 11/17/2022]
Abstract
Pesticide residual persistence in agriculture soil selectively increases the pesticide-degrading population and transfers the pesticide-degrading gene to other populations, leading to cross-resistance to a wide range of antibiotics. The enzymes that degrade pesticides can also catabolize the antibiotics by inducing changes in the gene or protein structure through induced mutations. The present work focuses on the pesticide-degrading bacteria isolated from an agricultural field that develop cross-resistance to antibiotics. This cross-resistance is developed through catabolic gene clusters present in an extrachromosomal plasmid. A larger plasmid (236.7 Kbp) isolated from Bacillus sp. was sequenced by next-generation sequencing, and important features such as α-β hydrolase, DNA topoisomerase, DNA polymerase III subunit beta, reverse transcriptase, plasmid replication rep X, recombination U, transposase, and S-formylglutathione hydrolase were found in this plasmid. Among these, the α-β hydrolase enzyme is known for the degradation of organophosphate pesticides. The cloning and expression of the α-β hydrolase gene imply nonspecific cleavage of antibiotics through a cross-resistance phenomenon in the host. The docking of α-β hydrolase with a spectrum of antibiotics showed a high G-score against chloramphenicol (-3.793), streptomycin (-2.865), cefotaxime (-5.885), ampicillin (-4.316), and tetracycline (-3.972). This study concludes that continuous exposure to pesticide residues may lead to the emergence of multidrug-resistant strains among the wild microbial flora.
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Affiliation(s)
| | - Murugan Athiappan
- Department of Microbiology, Periyar University, Salem, Tamil Nadu, India
| | | | - Javid A. Parray
- Department of Environmental Science, Government SAM Degree College Budgam, Jammu & Kashmir 191111, India
| | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, Jammu & Kashmir 190001, India
| | - K. N. Aruljothi
- Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, India
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, Egypt
| | - Abdulaziz A. Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Zhao X, Wang L, Ma F, Yang J. Characterisation of an efficient atrazine-degrading bacterium, Arthrobacter sp. ZXY-2: an attempt to lay the foundation for potential bioaugmentation applications. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:113. [PMID: 29692866 PMCID: PMC5905105 DOI: 10.1186/s13068-018-1113-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 04/10/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The isolation of atrazine-degrading microorganisms with specific characteristics is fundamental for bioaugmenting the treatment of wastewater containing atrazine. However, studies describing the specific features of such microorganisms are limited, and further investigation is needed to improve our understanding of bioaugmentation. RESULTS AND CONCLUSIONS In this study, strain Arthrobacter sp. ZXY-2, which displayed a strong capacity to degrade atrazine, was isolated and shown to be a potential candidate for bioaugmentation. The factors associated with the biodegrading capacity of strain ZXY-2 were investigated, and how these factors likely govern the metabolic characteristics that control bioaugmentation functionality was determined. The growth pattern of Arthrobacter sp. ZXY-2 followed the Haldane-Andrews model with an inhibition constant (Ki) of 52.76 mg L-1, indicating the possible augmentation of wastewater treatment with relatively high atrazine concentrations (> 50 ppm). Real-time quantitative PCR (RT-qPCR) results showed a positive correlation between the atrazine degradation rate and the expression levels of three functional genes (trzN, atzB, and atzC), which helped elucidate the role of strain ZXY-2 in bioaugmentation. In addition, multiple copies of the atzB gene were putatively identified, explaining the higher expression levels of this gene than those of the other functional genes. Multiple copies of the atzB gene may represent a compensatory mechanism that ensures the biodegradation of atrazine, a feature that should be exploited in future bioaugmentation applications.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Li Wang
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
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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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10
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Zhou Q, Chen L, Wang Z, Wang J, Ni S, Qiu J, Liu X, Zhang X, Chen X. Fast atrazine degradation by the mixed cultures enriched from activated sludge and analysis of their microbial community succession. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:22152-22157. [PMID: 28455570 DOI: 10.1007/s11356-017-9052-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
In this study, fast atrazine degradation by the mixed bacterial cultures from sewage sludge was investigated. The acquired activated cultures showed great capability in atrazine degradation. The biodegradation process was well fitted into a pseudo-first reaction kinetic model. Atrazine could inhibit the propagation of ammonium oxidation bacteria and nitrite oxidation bacteria, decreasing the ammonium removal rate and the accumulation of nitrite. Only 162-172 reads of Nitrosomonadaceae and no Nitrospirales were detected after atrazine was exposed to the mixed cultures. The bacterial community structures in the cultures under different inoculation conditions (with or without atrazine) were investigated to explore the mechanism of atrazine degradation. Our results show that the genera Thiobacillus and Ferruginibacter were the most possible candidates responsible for the degradation of atrazine.
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Affiliation(s)
- Qingxin Zhou
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Leilei Chen
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Zhibin Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, People's Republic of China
- College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Junhua Wang
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, People's Republic of China
| | - Jiying Qiu
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Xiaoyong Liu
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Xiang Zhang
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China
| | - Xiangyan Chen
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Deep Processing Technology of Agricultural Product, 202# Gongye North Road, Jinan, 250100, People's Republic of China.
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11
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Zhao X, Wang L, Ma F, Bai S, Yang J, Qi S. Pseudomonas sp. ZXY-1, a newly isolated and highly efficient atrazine-degrading bacterium, and optimization of biodegradation using response surface methodology. J Environ Sci (China) 2017; 54:152-159. [PMID: 28391924 DOI: 10.1016/j.jes.2016.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 06/07/2023]
Abstract
Atrazine, a widely used herbicide, is increasing the agricultural production effectively, while also causing great environmental concern. Efficient atrazine-degrading bacterium is necessary to removal atrazine rapidly to keep a safe environment. In the present study, a new atrazine-degrading strain ZXY-1, identified as Pseudomonas, was isolated. This new isolated strain has a strong ability to biodegrade atrazine with a high efficiency of 9.09mg/L/hr. Temperature, pH, inoculum size and initial atrazine concentration were examined to further optimize the degradation of atrazine, and the synthetic effect of these factors were investigated by the response surface methodology. With a high quadratic polynomial mathematical model (R2=0.9821) being obtained, the highest biodegradation efficiency of 19.03mg/L/hr was reached compared to previous reports under the optimal conditions (30.71°C, pH7.14, 4.23% (V/V) inoculum size and 157.1mg/L initial atrazine concentration). Overall, this study provided an efficient bacterium and approach that could be potentially useful for the bioremediation of wastewater containing atrazine.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Li Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shunwen Bai
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shanshan Qi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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12
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Zhao X, Wang L, Du L, Yang J, Dong J, Ma F. Optimization of culturing conditions for isolated Arthrobacter sp. ZXY-2, an effective atrazine-degrading and salt-adaptive bacterium. RSC Adv 2017. [DOI: 10.1039/c7ra04661h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The isolated strainArthrobactersp. ZXY-2 could biodegrade atrazine effectively with high salinity resistance.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Li Wang
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Linna Du
- Department of Agriculture and Biotechnology
- Wenzhou Vocational College of Science and Technology
- Wenzhou 325006
- China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Jing Dong
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
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13
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Marinho G, Barbosa B, Rodrigues K, Aquino M, Pereira L. Potential of the filamentous fungus Aspergillus niger AN 400 to degrade Atrazine in wastewaters. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Hatakeyama T, Takagi K. Bacterial biodegradation of melamine-contaminated aged soil: influence of different pre-culture media or addition of activation material. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14997-15002. [PMID: 27080407 DOI: 10.1007/s11356-016-6616-2] [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: 01/20/2016] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
This study aimed to investigate the biodegrading potential of Arthrobacter sp. MCO, Arthrobacter sp. CSP, and Nocardioides sp. ATD6 in melamine-contaminated upland soil (melamine: approx. 10.5 mg/kg dry weight) after 30 days of incubation. The soil sample used in this study had undergone annual treatment of lime nitrogen, which included melamine; it was aged for more than 10 years in field. When R2A broth was used as the pre-culture medium, Arthrobacter sp. MCO could degrade 55 % of melamine after 30 days of incubation, but the other strains could hardly degrade melamine (approximately 25 %). The addition of trimethylglycine (betaine) in soil as an activation material enhanced the degradation rate of melamine by each strain; more than 50 % of melamine was degraded by all strains after 30 days of incubation. In particular, strain MCO could degrade 72 % of melamine. When the strains were pre-cultured in R2A broth containing melamine, the degradation rate of melamine in soil increased remarkably. The highest (72 %) melamine degradation rate was noted when strain MCO was used with betaine addition.
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Affiliation(s)
- Takashi Hatakeyama
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Kazuhiro Takagi
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.
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15
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Andleeb S, Jiang Z, Rehman KU, Olajide EK, Ying Z. Influence of Soil pH and Temperature on Atrazine Bioremediation. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/s1006-8104(16)30043-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Bioremediation strategies for removal of residual atrazine in the boreal groundwater zone. Appl Microbiol Biotechnol 2015; 99:10249-59. [DOI: 10.1007/s00253-015-6828-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/02/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
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17
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Wang Z, Dai Y, Zhao Q, Li N, Zhou Q, Xie S. Nonylphenol biodegradation, functional gene abundance and bacterial community in bioaugmented sediment: effect of external carbon source. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:12083-12091. [PMID: 25874439 DOI: 10.1007/s11356-015-4509-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Nonylphenol (NP) biodegradation in river sediment using Stenotrophomonas strain Y1 and Sphingobium strain Y2 were proved to be an effective strategy to remediate NP pollution in our earlier study. The purpose of this study is to investigate the influence of glucose addition on their ability to degrade NP in both liquid cultures and sediment microcosms. The shift in bacterial community structure and relative abundance of NP degraders in sediment microcosms were characterized using terminal restriction fragment length polymorphism analysis. The proportion of NP-degrading alkB and sMO genes was assessed using quantitative polymerase chain reaction (PCR) assay. The growth of Stenotrophomonas strain Y1 and its NP biodegradation efficiency were inhibited by glucose supplementation, while the relative abundance of alkB gene increased. However, NP degradation, as well as the growth of added degraders and proportion of sMO gene, was enhanced in the glucose-amended sediment microcosms inoculated with Sphingobium strain Y2. Moreover, external glucose addition altered bacterial community structures in bioaugmented sediment microcosms, depending on the level of glucose dosage.
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Affiliation(s)
- Zhao Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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18
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Ma W, Nie C, Chen B, Cheng X, Lun X, Zeng F. Adsorption and biodegradation of three selected endocrine disrupting chemicals in river-based artificial groundwater recharge with reclaimed municipal wastewater. J Environ Sci (China) 2015; 31:154-163. [PMID: 25968269 DOI: 10.1016/j.jes.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/01/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
Endocrine disrupting chemical (EDC) pollution in river-based artificial groundwater recharge using reclaimed municipal wastewater poses a potential threat to groundwater-based drinking water supplies in Beijing, China. Lab-scale leaching column experiments simulating recharge were conducted to study the adsorption, biodegradation, and transport characteristics of three selected EDCs: 17β-estradiol (E2), 17α-ethinylestradiol (EE2) and bisphenol A (BPA). The three recharge columns were operated under the conditions of continual sterilization recharge (CSR), continual recharge (CR), and wetting and drying alternative recharge (WDAR). The results showed that the attenuation effect of the EDCs was in the order of WDAR>CR>CSR system and E2>EE2>BPA, which followed first-order kinetics. The EDC attenuation rate constants were 0.0783, 0.0505, and 0.0479 m(-1) for E2, EE2 and BPA in the CR system, respectively. The removal rates of E2, EE2, and BPA in the CR system were 98%, 96% and 92%, which mainly depended on biodegradation and were affected by water temperature. In the CR system, the concentrations of BPA, EE2, and E2 in soil were 4, 6 and 10 times higher than in the WDAR system, respectively. According to the DGGE fingerprints, the bacterial community in the bottom layer was more diverse than in the upper layer, which was related to the EDC concentrations in the water-soil system. The dominant group was found to be proteobacteria, including Betaproteobacteria and Alphaproteobacteria, suggesting that these microbes might play an important role in EDC degradation.
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Affiliation(s)
- Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
| | - Chao Nie
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Bin Chen
- School of Environment and Natural Resource, Renmin University of China, Beijing 100872, China
| | - Xiang Cheng
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Xiaoxiu Lun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Fangang Zeng
- School of Environment and Natural Resource, Renmin University of China, Beijing 100872, China
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19
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Fang H, Lian J, Wang H, Cai L, Yu Y. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils. JOURNAL OF HAZARDOUS MATERIALS 2015; 286:457-65. [PMID: 25603295 DOI: 10.1016/j.jhazmat.2015.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/16/2014] [Accepted: 01/03/2015] [Indexed: 05/21/2023]
Abstract
Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils.
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Affiliation(s)
- Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianjun Lian
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Huifang Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lin Cai
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China.
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20
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Mineralization of melamine and cyanuric acid as sole nitrogen source by newly isolated Arthrobacter spp. using a soil-charcoal perfusion method. World J Microbiol Biotechnol 2015; 31:785-93. [DOI: 10.1007/s11274-015-1832-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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21
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Dai Y, Li N, Zhao Q, Xie S. Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure. Biodegradation 2015; 26:161-70. [PMID: 25743701 DOI: 10.1007/s10532-015-9724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.
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Affiliation(s)
- Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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22
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Wang Z, Yang Y, Sun W, Dai Y, Xie S. Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:2342-2349. [PMID: 25277711 DOI: 10.1007/s11356-014-3625-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.
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Affiliation(s)
- Zhao Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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23
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Liao X, Chen C, Zhang J, Dai Y, Zhang X, Xie S. Dimethylamine biodegradation by mixed culture enriched from drinking water biofilter. CHEMOSPHERE 2015; 119:935-940. [PMID: 25280176 DOI: 10.1016/j.chemosphere.2014.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/26/2014] [Accepted: 09/05/2014] [Indexed: 06/03/2023]
Abstract
Dimethylamine (DMA) is one of the important precursors of drinking water disinfection by-product N-nitrosodimethylamine (NDMA). Reduction of DMA to minimize the formation of carcinogenic NDMA in drinking water is of practical importance. Biodegradation plays a major role in elimination of DMA pollution in the environment, yet information on DMA removal by drinking water biofilter is still lacking. In this study, microcosms with different treatments were constructed to investigate the potential of DMA removal by a mixed culture enriched from a drinking water biofilter and the effects of carbon and nitrogen sources. DMA could be quickly mineralized by the enrichment culture. Amendment of a carbon source, instead of a nitrogen source, had a profound impact on DMA removal. A shift in bacterial community structure was observed with DMA biodegradation, affected by carbon and nitrogen sources. Proteobacteria was the predominant phylum group in DMA-degrading microcosms. Microorganisms from a variety of bacterial genera might be responsible for the rapid DMA mineralization.
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Affiliation(s)
- Xiaobin Liao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chao Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiaojian Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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24
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Wang Z, Yang Y, He T, Xie S. Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment. Appl Microbiol Biotechnol 2014; 99:3259-68. [DOI: 10.1007/s00253-014-6222-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 12/07/2022]
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25
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Wang Z, Yang Y, Sun W, Xie S, Liu Y. Nonylphenol biodegradation in river sediment and associated shifts in community structures of bacteria and ammonia-oxidizing microorganisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 106:1-5. [PMID: 24836870 DOI: 10.1016/j.ecoenv.2014.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/17/2014] [Accepted: 04/19/2014] [Indexed: 06/03/2023]
Abstract
Nonylphenol (NP) is one of commonly detected contaminants in the environment. Biological degradation is mainly responsible for remediation of NP-contaminated site. Knowledge about the structure of NP-degrading microbial community is still very limited. Microcosms were constructed to investigate the structure of microbial community in NP-contaminated river sediment and its change with NP biodegradation. A high level of NP was significantly dissipated in 6-9 days. Bacteria and ammonia-oxidizing archaea (AOA) were more responsive to NP amendment compared to ammonia-oxidizing bacteria (AOB). Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes were the largest bacterial groups in NP-degrading sediment. Microorganisms from bacterial genera Brevundimonas, Flavobacterium, Lysobacter and Rhodobacter might be involved in NP degradation in river sediment. This study provides some new insights towards NP biodegradation and microbial ecology in NP-contaminated environment.
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Affiliation(s)
- Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Yuyin Yang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Weimin Sun
- Department of Environmental Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
| | - Yong Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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26
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Wan R, Wang Z, Xie S. Dynamics of communities of bacteria and ammonia-oxidizing microorganisms in response to simazine attenuation in agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 472:502-508. [PMID: 24317158 DOI: 10.1016/j.scitotenv.2013.11.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 06/02/2023]
Abstract
Autochthonous microbiota plays a crucial role in natural attenuation of s-triazine herbicides in agricultural soil. Soil microcosm study was carried out to investigate the shift in the structures of soil autochthonous microbial communities and the potential degraders associated with natural simazine attenuation. The relative abundance of soil autochthonous degraders and the structures of microbial communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. Phylogenetic composition of bacterial community was also characterized using clone library analysis. Soil autochthonous microbiota could almost completely clean up simazine (100 mg kg(-1)) in 10 days after herbicide application, indicating a strong self-remediation potential of agricultural soil. A significant increase in the proportion of s-triazine-degrading atzC gene was found in 6 days after simazine amendment. Simazine application could alter the community structures of total bacteria and ammonia-oxidizing archaea (AOA) and bacteria (AOB). AOA were more responsive to simazine application compared to AOB and bacteria. Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were the dominant bacterial groups either at the initial stage after simazine amendment or at the end stage of herbicide biodegradation, but Actinobacteria predominated at the middle stage of biodegradation. Microorganisms from several bacterial genera might be involved in simazine biodegradation. This work could add some new insights on the bioremediation of herbicides contaminated agricultural soils.
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Affiliation(s)
- Rui Wan
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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27
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Yang Y, Wang Z, Xie S. Aerobic biodegradation of bisphenol A in river sediment and associated bacterial community change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 470-471:1184-1188. [PMID: 24246941 DOI: 10.1016/j.scitotenv.2013.10.102] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/25/2013] [Accepted: 10/27/2013] [Indexed: 06/02/2023]
Abstract
Bisphenol A (BPA) is one of the commonly detected endocrine-disrupting chemicals in the environment. Biodegradation plays a major role in elimination of BPA pollution in the environment. However, information on the structure of BPA-degrading microbial community is still lacking. In this study, microcosms with different treatments were constructed to investigate the microbial community structure in river sediment and its shift during BPA biodegradation. BPA could be quickly depleted in the BPA-spiked sediment. BPA amendment had a significant impact on sediment bacterial community, influenced by dosage levels. Gammaproteobacteria and Alphaproteobacteria were the predominant bacterial groups in BPA-degrading sediment microcosm. A consortium of microorganisms from different bacterial genera might be involved in BPA biodegradation in river sediment. This study provides some new insights towards BPA biodegradation and microbial ecology in BPA-degrading environment.
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Affiliation(s)
- Yuyin Yang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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Wan R, Yang Y, Sun W, Wang Z, Xie S. Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:3175-3181. [PMID: 24194418 DOI: 10.1007/s11356-013-2268-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/21/2013] [Indexed: 06/02/2023]
Abstract
The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.
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Affiliation(s)
- Rui Wan
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing, 100871, China
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Guo Q, Wan R, Xie S. Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:337-343. [PMID: 23771408 DOI: 10.1007/s11356-013-1914-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.
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Affiliation(s)
- Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
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