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Chen T, Fu B, Li H. Optimisation of PAHs biodegradation by Klebsiella pneumonia and Pseudomonas aeruginosa through response surface methodology. ENVIRONMENTAL TECHNOLOGY 2024; 45:5204-5217. [PMID: 37970911 DOI: 10.1080/09593330.2023.2283813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023]
Abstract
Response Surface Methodology (RSM) with Box-Behnken Design (BBD) is used to optimise the Phenanthrene (PHE) degradation process by Klebsiella pneumoniae (K bacteria) and Pseudomonas aeruginosa (P bacteria). Wherein substrate concentration, temperature, and pH at three levels are used as independent variables, and degradation rate of PHE as dependent variables (response). The statistical analysis, via ANOVA, shows coefficient of determination R2 as 0.9848 with significant P value 0.0001 fitting in second-order quadratic regression model for PAHs removal by Klebsiella pneumonia, and R2 as 0.9847 with significant P value 0.0001 by P bacteria. According to the model analysis, temperature (P < 0.0006) is the most influential factor for PHE degradation efficiency by K bacteria, while pH (P < 0.0001) is the most influential factor for PHE degradation by P bacteria. The predicted optimum parameters for K bacteria, namely, temperature, substrate concentration, and pH are found to be 34.00℃, 50.80 mg/L, and 7.50, respectively, and those for P bacteria are 33.30℃, 52.70 mg/L, and 7.20, respectively. At these optimum conditions, the observed PHE removal rates by two bacteria are found to be 83.36% ± 2.1% and 81.23% ± 1.6% in validation experiments, respectively. Thus RSM can optimise the biodegradation conditions of both bacteria for PHE.
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Affiliation(s)
- Tao Chen
- Beijing University of Civil Engineering and Architecture, Key Laboratory of Urban Stormwater System & Water Environment Beijing, Beijing, China
| | - Bo Fu
- Beijing University of Civil Engineering and Architecture, Key Laboratory of Urban Stormwater System & Water Environment Beijing, Beijing, China
| | - Haiyan Li
- Tianjin Municipal Engineering Design and Research Institute Co. Ltd, Tianjin
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Li Y, Lu J, Dong C, Wang H, Liu B, Li D, Cui Y, Wang Z, Ma S, Shi Y, Wang C, Zhu X, Sun H. Physiological and biochemical characteristics and microbial responses of Medicago sativa (Fabales: Fabaceae) varieties with different resistance to atrazine stress. Front Microbiol 2024; 15:1447348. [PMID: 39220044 PMCID: PMC11363823 DOI: 10.3389/fmicb.2024.1447348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Atrazine, a commonly employed herbicide for corn production, can leave residues in soil, resulting in photosynthetic toxicity and impeding growth in subsequent alfalfa (Medicago sativa L.) crops within alfalfa-corn rotation systems. The molecular regulatory mechanisms by which atrazine affects alfalfa growth and development, particularly its impact on the microbial communities of the alfalfa rhizosphere, are not well understood. This study carried out field experiments to explore the influence of atrazine stress on the biomass, chlorophyll content, antioxidant system, and rhizosphere microbial communities of the atrazine-sensitive alfalfa variety WL-363 and the atrazine-resistant variety JN5010. The results revealed that atrazine significantly reduced WL-363 growth, decreasing plant height by 8.58 cm and root length by 5.42 cm (p < 0.05). Conversely, JN5010 showed minimal reductions, with decreases of 1.96 cm in height and 1.26 cm in root length. Chlorophyll content in WL-363 decreased by 35% under atrazine stress, while in JN5010, it was reduced by only 10%. Reactive oxygen species (ROS) accumulation increased by 60% in WL-363, compared to a 20% increase in JN5010 (p < 0.05 for both). Antioxidant enzyme activities, such as superoxide dismutase (SOD) and catalase (CAT), were significantly elevated in JN5010 (p < 0.05), suggesting a more robust defense mechanism. Although the predominant bacterial and fungal abundances in rhizosphere soils remained generally unchanged under atrazine stress, specific microbial groups exhibited variable responses. Notably, Promicromonospora abundance declined in WL-363 but increased in JN5010. FAPROTAX functional predictions indicated shifts in the abundance of microorganisms associated with pesticide degradation, resistance, and microbial structure reconstruction under atrazine stress, displaying different patterns between the two varieties. This study provides insights into how atrazine residues affect alfalfa rhizosphere microorganisms and identifies differential microbial responses to atrazine stress, offering valuable reference data for screening and identifying atrazine-degrading bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xiaoyan Zhu
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Hao Sun
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
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Sun S, Wei R, Hu S, Yang M, Ni J. Isolation and characterization of distinctive pyrene-degrading bacteria from an uncontaminated soil. Biodegradation 2024; 35:657-670. [PMID: 38279065 DOI: 10.1007/s10532-023-10065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024]
Abstract
Considerable efforts that isolate and characterize degrading bacteria for polycyclic aromatic hydrocarbons (PAHs) have focused on contaminated environments so far. Here we isolated three distinctive pyrene (PYR)-degrading bacteria from a paddy soil that was not contaminated with PAHs. These included a novel Bacillus sp. PyB-9 and efficient degraders, Shigella sp. PyB-6 and Agromyces sp. PyB-10. All three strains could utilize naphthalene, phenanthrene, anthracene, fluoranthene and PYR as sole carbon sources, and degraded PYR in a range of temperatures (27-37 °C) and pH (5-8). Strains PyB-6 and PyB-10 almost completely degraded 50 mg L-1 PYR within 15 days, and 75.5% and 98.9% of 100 mg L-1 PYR in 27 days, respectively. The kinetics of PYR biodegradation was well represented by the Gompertz model. Ten and twelve PYR metabolites were identified in PYR degradation process by strains PyB-6 and PyB-10, respectively. Chemical analyses demonstrated that the degradation mechanisms of PYR were the same for strains PyB-6 and PyB-10 with initial dioxygenation mainly on C-4,5 positions of PYR. The degradation of 4,5-phenanthrenedicarboxylic acid was branched to 4-phenanthrenecarboxylic acid pathway and 5-hydroxy-4-phenanthrenecarboxylic acid pathway, both of which played important roles in PYR degradation by strains PyB-6 and PyB-10. To our knowledge, Shigella sp. and Agromyces sp. were found for the first time to possess the capability for PAHs degradation. These findings contributed to upgrading the bank of microbial resource and knowledge on PAH biodegradation.
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Affiliation(s)
- Shanshan Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Ran Wei
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Siyi Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Meiyu Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Jinzhi Ni
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
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Ge H, Peng Z, Lu D, Yang Z, Li H. Biodegradation of high molecular weight polycyclic aromatic hydrocarbons by Sarocladium terricola strain PYR-233 isolated from petrochemical contaminated sediment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 363:121419. [PMID: 38852405 DOI: 10.1016/j.jenvman.2024.121419] [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: 10/27/2023] [Revised: 04/03/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) were frequently found in sediment and were primarily treated through microbial degradation. Thus, efficient management of PAH pollution requires exploring the molecular degradation mechanisms of PAHs and expanding the pool of available microbial resources. A fungus (identified as Sarocladium terricola strain RCEF778) with the remarkable ability to degrade pyrene was screened from sediment near a petrochemical plant, and its growth and pyrene degradation characteristics were comprehensively investigated. The results showed that the fungus exhibited great effectiveness in pyrene degradation, with a degradation ratio of 88.97% at 21 days at the conditions: 35 °C, pH 7, 10 mg L-1 initially pyrene concentration, 3% supplementary salt, and glucose supplementation. The generation and concentration variation of the intermediate products were identified, and the results revealed that the fungus degraded pyrene through two pathways: by salicylic acid and by phthalic acid. Three sediments (M1, M2, M3), each exhibiting different levels of PAH pollution, were employed to examine the effectiveness of fungal degradation of PAHs in practical sediment samples. These data showed that with the fungus, the degradation ratios ranged from 13.64% to 23.50% for 2-3 rings PAHs, 40.93%-49.41% for 4 rings PAHs, and 39.59%-48.07% for 5-6 rings PAHs, which were significantly higher than those for the sediment without the fungus and confirmed the excellent performance of the fungal. Moreover, the Gompertz model was employed to analyze the degradation kinetics of 4-rings and 5-6 rings PAHs in these sediments, and the results demonstrated that the addition of the fungus could significantly increase the maximum degradation ratio, degradation start-up rate and maximum degradation rate of 4-rings and 5-6 rings PAHs and shorten the time required to reach the maximum degradation rate. This study not only supplied fungal materials but also established crucial theoretical foundations for the development of bioremediation technologies aimed at high molecular weight PAH-contaminated sediments.
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Affiliation(s)
- Huanying Ge
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, PR China.
| | - Zhaoxia Peng
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, PR China
| | - Denglong Lu
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, PR China
| | - Zhaoguang Yang
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, PR China
| | - Haipu Li
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, PR China.
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Wang C, Zhang Y, Wang S, Lv X, Xu J, Zhang X, Yang Q, Meng F, Xu B. Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil. Front Microbiol 2024; 15:1383526. [PMID: 39040904 PMCID: PMC11261347 DOI: 10.3389/fmicb.2024.1383526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/24/2024] Open
Abstract
Objective Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process. Methods The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens. Results We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc. Conclusion This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.
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Affiliation(s)
- Can Wang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Yinghua Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shaoxiang Wang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Xia Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xueting Zhang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Qing Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fanlai Meng
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
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Li J, Hong M, Tang R, Cui T, Yang Y, Lv J, Liu N, Lei Y. Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum. ENVIRONMENTAL TECHNOLOGY 2024; 45:1497-1507. [PMID: 36384417 DOI: 10.1080/09593330.2022.2145914] [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: 07/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Phenanthrene, one of the polycyclic aromatic hydrocarbons, is stubborn and persistent and exists widely in petroleum-contaminated soil. Filamentous fungi are good assistants to bacterial transport, by hyphae passing through soil pores and reaching further positions. An isolated bacterial strain, from the contaminated soil of the coking plant, was identified as Diaphorobacter and named LW2, which could use phenanthrene as the only carbon source and energy for its growth. LW2 could degrade phenanthrene in a wide range of pH, temperature and initial concentration. When pH was 6 and 10, the removal rate of phenanthrene was 38.59% and 76.44%, respectively, and the removal rate of phenanthrene was 68.25% at 15 ℃. And LW2 could degrade 86.64% phenanthrene when the initial concentration was 100 mg L-1. The detection of DI-N-octyl phthalate, phthalic acid and p-hydroxybenzoic acid revealed that the strain LW2 metabolised phenanthrene through the phthalic acid pathway. Meanwhile, swimming and swarming test results suggested that LW2 was motile. The auxiliary effect of Pythium ultimum on LW2 migration was assessed. In the presence of Pythium ultimum, LW2 could migrate within the range of centimters by its mycelium, which was also observed by fluorescence microscopy. Meanwhile, the degradation ability of LW2 after the migration was also explored. The results proved that the migration process had no significant effect on its degradation ability, and LW2 still showed good phenanthrene metabolism ability. This study provides more possibilities for the bioremediation of phenanthrene-contaminated soil by screening the degradation bacteria and testing the effect of fungi on its migration.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Tingchen Cui
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Yadong Yang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Na Liu
- Institute of Groundwater and Earth Science, Jinan University, Guangzhou City, People's Republic of China
| | - Yutao Lei
- South China Institute of Environmental Sciences, MEP, Guangzhou, People's Republic of China
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Chen X, Zhu Y, Chen F, Li Z, Zhang X, Wang G, Ji J, Guan C. The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167305. [PMID: 37742959 DOI: 10.1016/j.scitotenv.2023.167305] [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: 08/03/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.
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Affiliation(s)
- Xiancao Chen
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Yalan Zhu
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Fenyan Chen
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhiman Li
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Xiaoge Zhang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
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Jiang J, Tian W, Lu Z, Chu M, Cao H, Zhang D. Cometabolic degradation of pyrene with phenanthrene as substrate: assisted by halophilic Pseudomonas stutzeri DJP1. Biodegradation 2023; 34:519-532. [PMID: 37354271 DOI: 10.1007/s10532-023-10035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
At present, cometabolic degradation is an extensive method for the biological removal of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) in the marine environment. However, due to the refractory to degradation and high toxicity, there are few studies on pyrene (PYR) cometabolic degradation with phenanthrene (PHE) as substrate. In this study, a Pseudomonas stutzeri DJP1 strain isolated from sediments was used in the cometabolic system of PHE and PYR. The biomass and the activity of key enzymes such as dehydrogenase and catechol 12 dioxygenase of strain were improved, but the enhancement of biotoxicity resulted in the inhibition of cometabolism simultaneously. Seven metabolites were identified respectively in PYR, PHE degradation cultures. It was speculated that the cometabolism of PHE and PYR had a common phthalic acid pathway, and the degradation pathway of PHE was included in the downstream pathway of PYR. The functional genes such as PhdF, NidD and CatA involved in DJP1 degradation were revealed by Genome analysis. This study provides a reference for the biodegradation of PYR and PHE in real marine environment.
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Affiliation(s)
- Junfeng Jiang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Weijun Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China.
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, People's Republic of China.
| | - Zhiyang Lu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Meile Chu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Huimin Cao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Dantong Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
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Fischer MS, Patel NJ, de Lorimier PJ, Traxler MF. Prescribed fire selects for a pyrophilous soil sub-community in a northern California mixed conifer forest. Environ Microbiol 2023; 25:2498-2515. [PMID: 37553729 DOI: 10.1111/1462-2920.16475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub-community composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.
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Affiliation(s)
- Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Neem J Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Phillip J de Lorimier
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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Chen R, Zhao Z, Xu T, Jia X. Microbial Consortium HJ-SH with Very High Degradation Efficiency of Phenanthrene. Microorganisms 2023; 11:2383. [PMID: 37894041 PMCID: PMC10609217 DOI: 10.3390/microorganisms11102383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/04/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as Pseudomonas sp., Stenotrophomonas sp., Delftia sp., Pseudomonas sp., Brevundimonas sp., Curtobacterium sp., and Microbacterium sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.
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Affiliation(s)
- Rui Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Zhenhua Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Tao Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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11
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Zhuang J, Zhang R, Zeng Y, Dai T, Ye Z, Gao Q, Yang Y, Guo X, Li G, Zhou J. Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery. Front Microbiol 2023; 14:1193189. [PMID: 37287448 PMCID: PMC10242060 DOI: 10.3389/fmicb.2023.1193189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Introduction Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. Methods In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Results Our results suggested soil microbial a-diversity decreased under high C10-C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10-C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. Discussion The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.
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Affiliation(s)
- Jugui Zhuang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Ruihuan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences, Beijing, China
| | - Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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12
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Gu H, Yan J, Liu Y, Yu X, Feng Y, Yang X, Lam SS, Naushad M, Li C, Sonne C. Autochthonous bioaugmentation accelerates phenanthrene degradation in acclimated soil. ENVIRONMENTAL RESEARCH 2023; 224:115543. [PMID: 36822540 DOI: 10.1016/j.envres.2023.115543] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Bioaugmentation helps to obtain a microbiome capable of remediating polycyclic aromatic hydrocarbons (PAHs). In this study, acclimation of microorganisms to soil supplemented with phenanthrene (PHE) led to enrichment with PAH-degraders, including those in Actinobacteriota and in the genera Streptomyces, Rhodococcus, Nocardioides, Sphingomonas, and Mycobacterium. Aqueous (28 °C, pH 6.5) and soil cultures inoculated with PHE-acclimated soil showed a high PHE (ca. 50 mg L-1) degradation efficiency. The PHE degradation kinetics in aqueous and soil incubations fitted to the Gompertz equation and the first-order kinetic equation, respectively. Indigenous microorganisms adapted to PHE in their environment, and this increased their capacity to degrade PHE. The effect of co-contaminants and pathway intermediates on PHE degradation showed that the degradation of PHE improved in the presence of diesel while being hindered by lubricant oil, catechol, salicylic and phthalic acid. Our findings provide theoretical and practical support for bioremediationof PAHs in the environment.
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Affiliation(s)
- Haiping Gu
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Jie Yan
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuhao Liu
- School of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Xuewei Yu
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Yan Feng
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuanyi Yang
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Center for Transdisciplinary Research, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Mu Naushad
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Cheng Li
- School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Christian Sonne
- Department of Ecoscience, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark.
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13
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Zheng Z, Liu W, Zhou Q, Li J, Zeb A, Wang Q, Lian Y, Shi R, Wang J. Effects of co-modified biochar immobilized laccase on remediation and bacterial community of PAHs-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130372. [PMID: 36444066 DOI: 10.1016/j.jhazmat.2022.130372] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Considering the stability and economy of immobilized enzymes, this study prepared co-modified biochar immobilized laccase product named Fe3O4@NaBC@GA@LC via orthogonal experimental design and explored its possibility of remediating polycyclic aromatic hydrocarbons (PAHs) contaminated soil in steel plants. Compared with the free laccase treatment, the relative activity of Fe3O4@NaBC@GA@LC remained 60 % after 50 days of incubation at room temperature. The relative activity of Fe3O4@NaBC@GA@LC could still retain nearly 80 % after five reuses. In the process of simulating the PAHs-contaminated site treatment experiment in Hangzhou Iron and steel plant, immobilized laccase exhibited efficient adsorption and degradation performances and even the removal rate of 5-ring PAHs reached more than 90 % in 40 days, resulting in improving urease activity and dehydrogenase in the soil and promoted the growth of a PAH degrading bacteria (Massilia). Our results further explained the efficient degradation effects of Fe3O4@NaBC@GA@LC on PAHs, which make it a promising candidate for PAHs-contaminated soil remediation.
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Affiliation(s)
- Zeqi Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Weitao Liu
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jiantao Li
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Aurang Zeb
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qi Wang
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yuhang Lian
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Ruiying Shi
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jianlin Wang
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education (MOE), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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14
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Zhang Y, Li X, Lu L, Huang F, Liu H, Zhang Y, Yang L, Usman M, Li S. Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees. Microorganisms 2023; 11:microorganisms11020233. [PMID: 36838198 PMCID: PMC9966171 DOI: 10.3390/microorganisms11020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.
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Affiliation(s)
- Yifang Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaomin Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Correspondence: (L.L.); (S.L.)
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Yu Zhang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Luhua Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Muhammad Usman
- PEIE Research Chair for the Development of Industrial Estates and Free Zones, Center for Environmental Studies and Research, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence: (L.L.); (S.L.)
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15
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Firoozbakht M, Sepahi AA, Rashedi H, Yazdian F. Investigating the effect of nanoparticle on phenanthrene biodegradation by Labedella gwakjiensis strain KDI. Biodegradation 2022; 33:441-460. [PMID: 35732966 DOI: 10.1007/s10532-022-09991-0] [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: 07/15/2021] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), as persistent organic contaminants, are a major source of concern due to their toxic effect on ecosystems and human health. This study attempted to isolate halotolerant PAHs degrading bacteria from saline oil-contaminated soils. Among the isolates, strain KDI with the highest 16S rRNA gene sequence similarity to Labedella gwakjiensis was able to reduce surface tension (ST) from 65.42 to 26.60 mN m-1 and increase the emulsification index to 81.04%, as a result of significant biosurfactant production. Response Surface Methodology (RSM) analysis was applied to optimize the factors, i.e. PAHs concentration and NaCl concentration as well as to determine the effect of these important variables on PAHs biodegradation. The Carbon Quantum Dots. Iron Oxide (CQDs.Fe3O4) nanoparticles were characterized by several popular analytical techniques, after which the effect of CQD.Fe3O4 nanoparticles on biodegradation was examined. PAHs biodegradation rate and efficiency of strain KDI to degrade PHE in the presence of CQD.Fe3O4 nanoparticles was analyzed by GC. According to the results during biodegradation both the concentration of PAHs and the amount of NaCl were effective. The biodegradation rate significantly increased in the presence of CQD.Fe3O4. The highest biodegradation of PHE occurred in the presence of 0.5 g/L of CQD.Fe3O4 which was 63.63% and 81.77% after 48 and 72 h of incubation. To the best of our knowledge, this is the first report on optimization of PAHs concentration and salinity by RSM and nanobioremediation of PHE using a bacterial strain in the presence of CQD.Fe3O4 nanoparticles.
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Affiliation(s)
- Maryam Firoozbakht
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abbas Akhavan Sepahi
- Department of Microbiology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran.
| | - Hamid Rashedi
- Department of Biotechnology, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
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16
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Luo C, Hu X, Bao M, Sun X, Li F, Li Y, Liu W, Yang Y. Efficient biodegradation of phenanthrene using Pseudomonas stutzeri LSH-PAH1 with the addition of sophorolipids: Alleviation of biotoxicity and cometabolism studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119011. [PMID: 35182655 DOI: 10.1016/j.envpol.2022.119011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Phenanthrene (PHE) is widely distributed, and it can cause genotoxicity in humans by interacting with enzymes in the body. A current challenge for PHE bioremediation is the inhibitory effect of biotoxic intermediates on bacterial growth. Notably, the aerobic biotransformation processes for PHE in the presence of sophorolipids have been poorly studied. Here, a PHE-degrading strain was isolated from sediments and identified as Pseudomonas stutzeri and named LSH-PAH1. It was observed that 1-naphthol (a biotoxic substance that can inhibit strain growth) was produced during the PHE metabolism process of LSH-PAH1. The biodegradation ratio increased from 21.4% to 91.7% within 48 h after the addition of sophorolipids. Unexpectedly, this addition accelerated the metabolic process for 1-naphthol rather than causing its accumulation. The cometabolism of 1-naphthol and sophorolipids alleviated the biotoxic effects for the strain, which was verified by gene expression analysis. We identified a new PHE-degrading strain and provided a mechanism for PHE biodegradation using LSH-PAH1 with the addition of sophorolipids, which provides a reference for practical applications of the bioremediation of PHE and study of the cometabolism of biotoxic intermediates.
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Affiliation(s)
- Chengyi Luo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Xin Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China.
| | - Xiaojun Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Fengshu Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Yiming Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Wenxiu Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, PR China
| | - Yan Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, PR China
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17
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Lee YY, Lee SY, Lee SD, Cho KS. Seasonal Dynamics of Bacterial Community Structure in Diesel Oil-Contaminated Soil Cultivated with Tall Fescue ( Festuca arundinacea). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084629. [PMID: 35457496 PMCID: PMC9025128 DOI: 10.3390/ijerph19084629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 11/18/2022]
Abstract
The objective of this study was to explore the seasonal characteristics of rhizoremediation and the bacterial community structure over the course of a year in soil contaminated with diesel oil. The soil was contaminated with diesel oil at a total petroleum hydrocarbon (TPH) concentration of 30,000 mg-TPH·kg-soil−1. Tall fescue seedlings were planted in the contaminated soil and rhizoremediation performance was monitored for 317 days. The TPH concentration gradually declined, reaching 75.6% after day 61. However, the TPH removability decreased by up to 30% after re-contamination in the fall and winter. The bacterial community structure exhibited distinct seasonal dynamics. Genus Pseudomonas significantly increased up to 55.7% in the winter, while the genera Immundisolibacter and Lysobacter, well-known petroleum hydrocarbon (PH)-degrading bacteria, were found to be positively linked to the TPH removal rate. Consequently, knowledge of this seasonal variation in rhizoremediation performance and the bacterial community structure is useful for the improvement of rhizoremediation in PH-contaminated environments.
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Affiliation(s)
| | | | | | - Kyung-Suk Cho
- Correspondence: ; Tel.: +82-2-3277-2393; Fax: +82-2-3277-3275
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18
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Fan R, Tian H, Wu Q, Yi Y, Yan X, Liu B. Mechanism of bio-electrokinetic remediation of pyrene contaminated soil: Effects of an electric field on the degradation pathway and microbial metabolic processes. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126959. [PMID: 34449353 DOI: 10.1016/j.jhazmat.2021.126959] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
In this study, the mechanism of bio-electrokinetic (BIO-EK) remediation to improve the degradation of pyrene was evaluated based on an analysis of the intermediate products and the microbial community. The results show that BIO-EK remediation has a higher pyrene degradation efficiency on pyrene and its intermediate products than the bioremediation and electrokinetic (EK) remediation processes. A series of intermediate products were detected. According to the type of the intermediate products, two degradation pathways, biological metabolism and electrochemical oxidation, are proposed in the BIO-EK remediation of pyrene. Furthermore, the primary microbial taxa involved in the pollutant degradation changed, which led to variations in the functional gene components. The abundant and functional genes related to metabolism were specifically analyzed. The results indicate that the electric field promotes the expression of metabolisms associated with 14 carbohydrates, 13 lipids, 13 amino acids, five energies, and in particular, 11 xenobiotics. These results suggest that in addition to the promotion effect on the microbial metabolism caused by the electric field, BIO-EK remediation can promote the degradation of pollutants due to the coexistence of a microbial metabolic pathway and an electrochemical oxidation pathway.
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Affiliation(s)
- Ruijuan Fan
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan 750021, China.
| | - Haihua Tian
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China
| | - Qiong Wu
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China
| | - Yuanyuan Yi
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China
| | - Xingfu Yan
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan 750021, China
| | - Bingru Liu
- School of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan 750021, China
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19
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Yang H, Zhang Y, Chuang S, Cao W, Ruan Z, Xu X, Jiang J. Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1559-1571. [PMID: 33443714 DOI: 10.1007/s10646-020-02336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.
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Affiliation(s)
- Hongxing Yang
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environment, Anhui Science and Technology University, Anhui, 233100, China
| | - Yanlin Zhang
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaochuang Chuang
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhepu Ruan
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Gu H, Yan K, You Q, Chen Y, Pan Y, Wang H, Wu L, Xu J. Soil indigenous microorganisms weaken the synergy of Massilia sp. WF1 and Phanerochaete chrysosporium in phenanthrene biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146655. [PMID: 33798893 DOI: 10.1016/j.scitotenv.2021.146655] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Biodegradation is a promising way to reduce phenanthrene (PHE) in environment. PHE biodegradation by bioaugmentation of axenic and mixed cultures of Massilia sp. WF1 (a highly efficient PHE-degrading bacteria) and Phanerochaete chrysosporium (P. chrysosporium, an extensively researched model fungus in organic pollutant bioremediation) was investigated in aqueous and autoclaved/un-autoclaved soil cultures. In the liquid cultures, the strain WF1 could use PHE (ca. 10 mg L-1) as the sole carbon source, and the presence of d-fructose (500 mg L-1) had no obvious effect on its PHE degradation; while the opposite was observed for P. chrysosporium. The bioaugmentation of strain WF1 and P. chrysosporium co-culture showed the highest PHE-degradation efficiency, especially in the aqueous and the autoclaved soil (PHE, ca. 50 mg kg-1) cultures, indicating a synergistic interaction of the co-culture during PHE dissipation. It was further observed that the indigenous microorganisms (mainly the Gram-positive bacteria) played a dominant role during PHE biodegradation and showed an antagonistic action against the strain WF1-P. chrysosporium co-culture, which weakened the synergistic action of the co-culture in the un-autoclaved soil. Besides, the abundances of PAH-RHDα GP and nidA genes were negatively correlated with residual PHE in the soil. Our findings provide the scientific support for bioremediation of PAHs in environment.
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Affiliation(s)
- Haiping Gu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China; Department of Environmental Sciences, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Kang Yan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Qi You
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yuanzhi Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China; Beihai Tieshangang District Human Resources and Social Security Bureau, Beihai, China
| | - Yunhui Pan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China; Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
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21
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Abstract
To increase the genomic data available for antibiotic discovery, three independently isolated antibiotic-producing Massilia strains were sequenced. No more than 84% average nucleotide identity was shared with publicly available Massilia genomes, and a low similarity of predicted biosynthetic gene clusters to known clusters was found.
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22
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Rong L, Zheng X, Oba BT, Shen C, Wang X, Wang H, Luo Q, Sun L. Activating soil microbial community using bacillus and rhamnolipid to remediate TPH contaminated soil. CHEMOSPHERE 2021; 275:130062. [PMID: 33667768 DOI: 10.1016/j.chemosphere.2021.130062] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Soil petroleum contamination has become a global environmental problem. In order to develop a new soil remediation technology, this study established bacteria isolation, surfactant toxicity matching and petroleum contaminated soil remediation practice. The simulated field remediation showed that inoculating the soil with Bacillus methylotrophicus and adding 500 mg kg-1 rhamnolipid (N + RL) to soil can remove 80.24% of aged total petroleum hydrocarbons (TPHs) within 30 days. In particular, although the remediated soil has inoculated sufficient bacterial suspension, the microbial abundance of Bacillus was not a significantly dominant genus after remediation, especially in N + RL (0.73% of the total), but the colonies of indigenous petroleum-degrading bacteria (such as Massilia and Streptomyces) increased significantly. The interaction among genera has been further proved to drive soil non-specific oxidases (such as polyphenol oxidase, laccase and catalase) to remove TPHs. This indicates that the interaction among microorganisms, rather than the degradability of exogenous degrading bacteria, plays more critical role in the degradation of organic pollutants, which enriches the traditional understanding of micro-remediation of contaminated soil. It can be concluded from the obtained results that the remediation of pollutants can be achieved by adjusting the purification capacity of the microbial community and the natural environment.
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Affiliation(s)
- Luge Rong
- School of Environment, Shenyang University, Shenyang, 110044, China
| | - Xuehao Zheng
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
| | - Belay Tafa Oba
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Chenbo Shen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Xiaoxu Wang
- School of Environment, Shenyang University, Shenyang, 110044, China
| | - Hui Wang
- School of Environment, Shenyang University, Shenyang, 110044, China
| | - Qing Luo
- School of Environment, Shenyang University, Shenyang, 110044, China
| | - Lina Sun
- School of Environment, Shenyang University, Shenyang, 110044, China.
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23
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Lara-Moreno A, Morillo E, Merchán F, Villaverde J. A comprehensive feasibility study of effectiveness and environmental impact of PAH bioremediation using an indigenous microbial degrader consortium and a novel strain Stenotrophomonas maltophilia CPHE1 isolated from an industrial polluted soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112512. [PMID: 33848881 DOI: 10.1016/j.jenvman.2021.112512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/04/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic Aromatic Hydrocarbons (PAHs) are major toxic and recalcitrant pollutants in the environment. This study assessed the capacity of an isolated soil microbial consortium (OMC) to biodegrade PAHs. OMC was able to reach 100% biodegradation of naphthalene, acenaphthylene, acenaphthene, fluorene and phenanthrene in solution, and up to 76% and 50% of anthracene and fluoranthene, respectively, from a mix of 16 PAHs. To measure phenanthrene (PHE) mineralization, OMC and eight strains isolated from OMC were used and identified by PCR amplification of the gene 16S ribosomal RNA. A novel Stenotrophomonas maltophilia CPHE1, not previously described as a PAH degrader, was able to mineralize almost 40% PHE and biodegrade 90.5% in solution, in comparison to OMC that reached 100% PHE degradation, but only 18.8% mineralization. Based on metabolites identified during PHE degradation and on the detection of two genes (PAH RHDα and nahAc) in OMC consortium, two possible via were described for its degradation, through salicylic and phthalic acid. PAH RHDα, which codified the first step on PHE biodegradation pathway, was also found in the DNA of S. maltophilia CPHE1. An ecotoxicology study showed that PHE bioremediation after inoculating S. maltophilia CPHE1 for 30 days decreased by half the solution toxicity.
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Affiliation(s)
- Alba Lara-Moreno
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain; Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain.
| | - Esmeralda Morillo
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain
| | - Francisco Merchán
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Jaime Villaverde
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain
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24
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Cavé-Radet A, Correa-Garcia S, Monard C, El Amrani A, Salmon A, Ainouche M, Yergeau É. Phenanthrene contamination and ploidy level affect the rhizosphere bacterial communities of Spartina spp. FEMS Microbiol Ecol 2021; 96:5895320. [PMID: 32821911 DOI: 10.1093/femsec/fiaa156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These events have resulted in a heightened tolerance to hydrocarbon contaminants, but the effects of this phenomenon on the rhizosphere microbial communities are unknown. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene was amplified and sequenced, whereas the abundances of the genes encoding for the PAH (polycyclic aromatic hydrocarbon) ring-hydroxylating dioxygenase (RHD) of Gram-negative and Gram-positive bacteria were quantified by real-time PCR. Both the contamination and the plant genotype significantly affected the bacterial communities. In particular, the allopolyploid S. anglica harbored a more diverse bacterial community in its rhizosphere. The interspecific hybrid and the allopolyploid also harbored significantly more copies of the PAH-RHD gene of Gram-negative bacteria in their rhizosphere than the parental species, irrespective of the contamination treatments. Overall, our results are showing that the recent polyploidization events in the Spartina affected its rhizosphere bacterial communities, both under normal and contaminated conditions, possibly increasing its phytoremediation potential.
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Affiliation(s)
- Armand Cavé-Radet
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Sara Correa-Garcia
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Cécile Monard
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Abdelhak El Amrani
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Armel Salmon
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Malika Ainouche
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Étienne Yergeau
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
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25
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Rajkumari J, Choudhury Y, Bhattacharjee K, Pandey P. Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community. Front Microbiol 2021; 12:593023. [PMID: 33708179 PMCID: PMC7940843 DOI: 10.3389/fmicb.2021.593023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/18/2021] [Indexed: 11/27/2022] Open
Abstract
The non-clinical Klebsiella pneumoniae variants, isolated from different environments, are now well acknowledged for their role in plant-growth promotion and biodegradation of pollutants. In the present study, a non-clinical environmental isolate K. pneumoniae AWD5 is being described for rhizoremediation of pyrene, applied through the rhizosphere of an ornamental plant, Tagetes erecta L (marigold). The non-pathogenic nature of AWD5 was established using an in vivo mouse model experiment, where AWD5 was unable to cause lung infection in tested mice. Degradation of pyrene, in the presence of succinate as co-substrate, was observed to be 87.5% by AWD5, after 21 days of incubation in minimal (Bushnell–Hass) medium in vitro conditions. Consequently, the bacterial inoculation through the rhizosphere of T. erecta L. plants resulted in 68.61% degradation of pyrene, which was significantly higher than control soil. Inoculation of AWD5 also improved plant growth and exhibited an increase in root length (14.64%), dry root weight (80.56%), shoot length (3.26%), and dry shoot weight (45.35%) after 60 days of incubation. T. erecta L., an ornamental plant, was also found to be suitable for bioremediation of pyrene. The effect of AWD5 application, and rhizoremediation process, on rhizosphere bacterial diversity and community structure has been studied using the metagenomic analysis of the 16S (V3–V4) region of rRNA. 37 bacterial phyla constituted the core microbiome, which was dominated by Proteobacteria followed by Actinobacteria, Actinobacteria, and Planctomycetes for all the treatments. AWD5 inoculation enhanced the relative abundance of Firmicutes and Acidobacteria as compared with other treatments. Genus Kaistobacter and Verrucomicrobia were found to be an abundant indigenous population in pyrene-spiked soils. Bacterial richness and diversity were analyzed using the Shannon–Wiener (H) index. A lower diversity index was observed in pyrene-spiked soils. Canonical correspondence analysis (CCA) showed a possible linkage with plant growth attributes and available nitrogen content that influences diversity and abundance of the bacterial community.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, India
| | | | | | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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26
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Sun S, Wang H, Yan K, Lou J, Ding J, Snyder SA, Wu L, Xu J. Metabolic interactions in a bacterial co-culture accelerate phenanthrene degradation. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123825. [PMID: 33264917 DOI: 10.1016/j.jhazmat.2020.123825] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/03/2020] [Accepted: 08/25/2020] [Indexed: 05/22/2023]
Abstract
A highly eff ;ective phenanthrene (PHE)-degrading co-culture containing Rhodococcus sp. WB9 and Mycobacterium sp. WY10 was constructed and completely degraded 100 mg L-1 PHE within 36 h, showing improved degradation rate compared to their monocultures. In the co-culture, strain WY10 played a predominant role in PHE degradation. 1-hydroxy-2-naphthoic acid was an end-product of PHE degradation by strain WB9 and accumulated in the culture medium to serve as a substrate for strain WY10 growth, thereby accelerating PHE degradation. In turn, strain WY10 degraded PHE and 1-hydroxy-2-naphthoic acid intracellularly to form phthalate and protocatechuate that were exported to the culture medium through efflux transporters. However, strain WY10 cannot take up extracellular phthalate due to the absence of phthalate transporters, restricting phthalate degradation and PHE mineralization. In the co-culture, phthalate and protocatechuate accumulated in the culture medium were taken up and degraded towards TCA cycle by strain WB9. Therefore, the metabolic cross-feeding of strains WB9 and WY10 accelerated PHE degradation and mineralization. These findings exhibiting the synergistic degradation of PHE in the bacterial co-culture will facilitate its bioremediation application.
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Affiliation(s)
- Shanshan Sun
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Kang Yan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Jun Lou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Jiahui Ding
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Shane A Snyder
- Nanyang Environment and Water Research Institute (NEWRI), Nanyang Technological University, Singapore 637141, Singapore
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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27
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Wang P, Zhang Y, Jin J, Wang T, Wang J, Jiang B. A high-efficiency phenanthrene-degrading Diaphorobacter sp. isolated from PAH-contaminated river sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140455. [PMID: 32758981 DOI: 10.1016/j.scitotenv.2020.140455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical persistent organic pollutants that accumulate in the environment, mainly from anthropogenic activities. Microbial degradation is the main pathway of PAHs degradation in the natural environment. Therefore, the widen of the available bank of microbial resources and exploration of the molecular degradation mechanisms of PAHs are crucial to the proper management of PAHs-polluted sites. In this work, a bacterial strain, YM-6, which has a high ability to utilize phenanthrene (PHE) as its sole source of carbon and energy, was isolated from sediment contaminated with PAHs. The strain YM-6 was found to degrade 96.3% of 100 mg/L of PHE in liquid cultures within 52 h. The strain was identified as Diaphorobacter sp. by 16S rDNA sequencing. The optimum growth conditions of the YM-6 strain were studied, and the results indicated that the optimum growth temperature of the strain was 30 °C, and the optimum growth pH was 7. The stain is well-suited for high-temperature stress (40 °C), and it could withstand 400 mg/L of PHE. The strain's PHE metabolism was assayed using GC-MS analyses. The results revealed that the YM-6 strain metabolized PHE via the phthalic acid pathway because the intermediates, such as phthalic acid, diethyl ester and phthalaldehydic acid, methyl ester, were detected. The use of this strain may be an attractive alternative for the bioremediation of polycyclic aromatic hydrocarbons in an aquatic environment.
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Affiliation(s)
- Ping Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China; Engineering Research Center of Biomembrane Water Purification and Utilization Technology, Ministry of Education, Maanshan 243002, China.
| | - Yongmin Zhang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Jie Jin
- Appraisal Center for Environment & Engineering, Ministry of Ecology and Environment,Beijing 100012,China
| | - Tianhui Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Jie Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Bingyu Jiang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
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28
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Mishra A, Rathour R, Singh R, Kumari T, Thakur IS. Degradation and detoxification of phenanthrene by actinobacterium Zhihengliuella sp. ISTPL4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27256-27267. [PMID: 31172432 DOI: 10.1007/s11356-019-05478-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are universal environmental contaminants of great concern with regard to their potential exposure and deleterious effect on human health. The current study is the first report of phenanthrene degradation by a psychrotolerant (15 °C), halophilic (5% NaCl), and alkalophilic (pH 8) bacterial strain Zhihengliuella sp. ISTPL4, isolated from the sediment sample of the Pangong Lake, Ladakh, Jammu and Kashmir, India. Degradation studies revealed that the optimum specific growth rate was observed at 250 ppm of phenanthrene with 81% and 87% removal of phenanthrene in 72 h and 168 h, respectively. During the degradation of phenanthrene; 9,10-dihydrophenanthrene; 1-phenanthrenecarboxylic acid; and phthalic acid were detected as intermediates. Whole-genome sequencing of strain ISTPL4 has predicted phenanthrene; 9,10-monooxygense; and epoxide hydrolase B that are involved in the phenanthrene metabolism. Phenanthrene cytotoxicity was evaluated with human hepatic carcinoma cell line (HepG2) and it was observed that the cytotoxicity decreased with increased duration of bacterial incubation and maximum cell viability was observed at 168 h (89.92%). Our results suggest, Zhihengliuella sp. ISTPL4 may promise a great potential for environmental remediation applications.
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Affiliation(s)
- Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rashmi Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi, 110007, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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29
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Metagenomic insights into microbial characterizations in explaining the distinction of biofilter performance during start-up. Biodegradation 2020; 31:183-199. [PMID: 32462278 DOI: 10.1007/s10532-020-09902-1] [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: 09/25/2019] [Accepted: 05/13/2020] [Indexed: 11/25/2022]
Abstract
As an effective alternative for dissolved nitrogen removal, biofilter closely associates its treatment performance to structural and/or operational conditions. In this study, a set of four different biofilters including MAVF (mature aerated vertical flow), NAVF (new aerated vertical flow), NVF (new non-aerated vertical flow), and BHF (baffled non-aerated horizontal flow) were employed to purify low C/N ratio (3.8) domestic wastewater. All the filters were packed with round ceramsite operated under varying hydraulic loading rates (HLRs) of 0.024-0.18 m/day. During the start-up, both the physicochemical and microbial characterizations were investigated. It was found that, carbon and nitrogen could achieve ideal removal in MAVF once added with further sedimentation, while phosphorus displayed an unsatisfactory sequestration in any of the four filters probably due to the high inflow load and/or lack of alternate anaerobic/aerobic conditions. Filter clustering based on percent removal and removal rate constant displayed a consistent pattern, which was similar to that based on taxa of phylum from 16S rRNA sequencing, or phylum/genus/species from shotgun metagenomic sequencing although there were obvious distinctions in taxa compositions among direct comparison. Meanwhile, gene function annotation revealed that filter clustering based on metabolic pathways was consistent with that based on purification performance. These consistencies might imply that the treatment performance was mainly determined by microbial degradation. The enrichment of specific functional microbes responsible for the degradation of certain pollutants, such as carbohydrates, matched well with the defined purification performance.
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30
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Kashyap N, Roy K, Moholkar VS. Mechanistic investigations in ultrasound-assisted biodegradation of phenanthrene. ULTRASONICS SONOCHEMISTRY 2020; 62:104890. [PMID: 31796330 DOI: 10.1016/j.ultsonch.2019.104890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 05/16/2023]
Abstract
This study has addressed the biodegradation of polycyclic aromatic hydrocarbon, phenanthrene using Candida tropicalis. Optimization using central composite statistical design yielded optimum experimental parameters as: pH = 6.2, temperature = 33.4 °C, mechanical shaking = 190 rpm and % inoculum = 9.26% v/v. Sonication of biodegradation mixture at 33 kHz and 10% duty cycle in log phase (12 h per day for 4 days) resulted in a 25% enhancement in phenanthrene removal. Profiles of specific growth rate (µ) and specific degradation rate (q) versus initial substrate concentration were fitted to Haldane substrate inhibition model. Both µ and q showed maxima for initial concentration of 100 mg L-1. Kinetic analysis of degradation profiles showed higher biomass yield coefficient and smaller decay coefficient in presence of sonication. Expression of total intracellular proteins in control and test experiments were analyzed using SDS-PAGE. This analysis revealed overexpression of enzyme catechol 2,3-dioxygenase (in meta route metabolism) during sonication which is involved in ring cleavage of phenanthrene. Evaluation of cell viability after sonication by flow cytometry analysis revealed > 80% live cells. These effects are attributed to enhanced cellular transport induced by intense microturbulence generated by sonication.
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Affiliation(s)
- Niharika Kashyap
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Kuldeep Roy
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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31
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Shon JC, Noh YJ, Kwon YS, Kim JH, Wu Z, Seo JS. The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110254. [PMID: 32007746 DOI: 10.1016/j.ecoenv.2020.110254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
The direct interactions of bacterial membranes and polycyclic aromatic hydrocarbons (PAHs) strongly influence the biological processes, such as metabolic activity and uptake of substrates due to changes in membrane lipids. However, the elucidation of adaptation mechanisms as well as membrane phospholipid alterations in the presence of phenanthrene (PHE) from α-proteobacteria has not been fully explored. This study was conducted to define the degradation efficiency of PHE by Sphingopyxis soli strain KIT-001 in a newly isolated from Jeonju river sediments and to characterize lipid profiles in the presence of PHE in comparison to cells grown on glucose using quantitative lipidomic analysis. This strain was able to respectively utilize 1-hydroxy-2-naphthoic acid and salicylic acid as sole carbon source and approximately 90% of PHE (50 mg/L) was rapidly degraded via naphthalene route within 1 day incubation. In the cells grown on PHE, strain KIT-001 appeared to dynamically change profiles of metabolite and lipid in comparison to cells grown on glucose. The levels of primary metabolites, phosphatidylethanolamines (PE), and phosphatidic acids (PA) were significantly decreased, whereas the levels of phosphatidylcholines (PC) and phosphatidylglycerols (PG) were significantly increased. The adaptation mechanism of Sphingopyxis sp. regarded mainly the accumulation of bilayer forming lipids and anionic lipids to adapt more quickly under restricted nutrition and toxicity condition. Hence, these findings are conceivable that strain KIT-001 has a good adaptive ability and biodegradation for PHE through the alteration of phospholipids, and will be helpful for applications for effective bioremediation of PAHs-contaminated sites.
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Affiliation(s)
- Jong Cheol Shon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Ji Noh
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Sang Kwon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Zhexue Wu
- Mass Spectrometry Convergence Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Su Seo
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea.
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Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. CHEMOSPHERE 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [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: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
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Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
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Sun S, Wang H, Fu B, Zhang H, Lou J, Wu L, Xu J. Non-bioavailability of extracellular 1-hydroxy-2-naphthoic acid restricts the mineralization of phenanthrene by Rhodococcus sp. WB9. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135331. [PMID: 31831232 DOI: 10.1016/j.scitotenv.2019.135331] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
Rhodococcus sp. WB9, a strain isolated from polycyclic aromatic hydrocarbons contaminated soil, degraded phenanthrene (PHE, 100 mg L-1) completely within 4 days. 18 metabolites were identified during PHE degradation, including 5 different hydroxyphenanthrene compounds resulted from multiple routes of initial monooxygenase attack. Initial dioxygenation dominantly occurred on 3,4-C positions, followed by meta-cleavage to form 1-hydroxy-2-naphthoic acid (1H2N). More than 95.2% of 1H2N was transported to and kept in extracellular solution without further degradation. However, intracellular 1H2N was converted to 1,2-naphthalenediol that was branched to produce salicylate and phthalate. Furthermore, 131 genes in strain WB9 genome were related to aromatic hydrocarbons catabolism, including the gene coding for salicylate 1-monooxygenase that catalyzed the oxidation of 1H2N to 1,2-naphthalenediol, and complete gene sets for the transformation of salicylate and phthalate toward tricarboxylic acid (TCA) cycle. Metabolic and genomic analyses reveal that strain WB9 has the ability to metabolize intracellular 1H2N to TCA cycle intermediates, but the extracellular 1H2N can't enter the cells, restricting 1H2N bioavailability and PHE mineralization.
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Affiliation(s)
- Shanshan Sun
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Binxin Fu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Hao Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Jun Lou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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Li X, Song Y, Yao S, Bian Y, Gu C, Yang X, Wang F, Jiang X. Can biochar and oxalic acid alleviate the toxicity stress caused by polycyclic aromatic hydrocarbons in soil microbial communities? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133879. [PMID: 31425980 DOI: 10.1016/j.scitotenv.2019.133879] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
It remains unclear whether biochar amendment can mediate changes in soil microbial communities caused by organic contaminants in the rhizosphere. In this study, phenanthrene-contaminated soil was amended with biochar and oxalic acid (OA) alone or in combination and incubated for 21 days. Phospholipid fatty acids (PLFAs) and high-throughput sequencing were used to evaluate shifts in bacterial and fungal community structure. Phenanthrene stress led to significant shifts in both soil bacterial and fungal community structure, in particularly, 82% of microbial phyla decreased in abundance. Biochar and/or OA improved the phenanthrene-polluted soil by positively mediating shifts in soil microbial communities stressed by phenanthrene. Specifically, biochar and/or OA led to the survival of certain microbial taxa that were inhibited by phenanthrene stress. In addition, many functional microbial individuals and genes participating in polycyclic aromatic hydrocarbon (PAH) degradation were positively stimulated by high phenanthrene stress and further stimulated by the simultaneous application of biochar and OA. Based on these findings, tandem biochar and rhizoremediation may be a feasible strategy for relieving PAH toxicity to soil microbial communities.
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Affiliation(s)
- Xiaona Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Shi Yao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglun Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
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Lemmel F, Maunoury-Danger F, Leyval C, Cébron A. DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils. FEMS Microbiol Ecol 2019; 95:5626340. [PMID: 31730156 DOI: 10.1093/femsec/fiz181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/13/2019] [Indexed: 11/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
| | - Florence Maunoury-Danger
- Université de Lorraine, CNRS, LIEC UMR7360, Campus Bridoux, Avenue du général Delestraint, 57070 Metz, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
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The Soil Microbiome of the Laurel Forest in Garajonay National Park (La Gomera, Canary Islands): Comparing Unburned and Burned Habitats after a Wildfire. FORESTS 2019. [DOI: 10.3390/f10121051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The evergreen laurel forest is a relic of ancient subtropical/tropical forests, of which the best remnant in the Canary Islands is in Garajonay National Park, on La Gomera island. The soil microbiome associated with a mature undisturbed (unburned) laurel forest was characterized at two locations at different topographical positions on the mountain: The slope and the ridge crest. Given the unusual circumstance of an intense wildfire that severely affected part of this forest, the burned soils were also studied. The soil in undisturbed areas was relatively uniform. The bacterial community composition was dominated by bacteria from phyla Proteobacteria, Acidobacteria, and Actinobacteria. The wildfire changed the composition of the bacterial communities. The Acidobacteria, Actinobacteria, and Alphaproteobacteria (dominant class in unburned forests) significantly decreased in burned soils along with a parallel high increase in Betaproteobacteria, Bacteroidetes, and Firmicutes. We further showed the dramatic effect of a wildfire on the soil microbiome of the laurel forest, appearing as a loss of species richness and diversity, species dominance, and changes in the composition of the bacterial communities.
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Wei C, Ren P, Cen Q, Zhu Y, Zhang Y. Simultaneous determination of dissolved phenanthrene and its metabolites by derivative synchronous fluorescence spectrometry with double scans method in aqueous solution. Talanta 2019; 195:339-344. [PMID: 30625553 DOI: 10.1016/j.talanta.2018.11.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 12/30/2022]
Abstract
A simple and sensitive derivative synchronous fluorescence spectrometry with double scans (DS-DSFS) method was developed for simultaneous determination of dissolved Phenanthrene (Phe) and its metabolites 1-hydroxy-2-naphthoic acid (1H2NA) and salicylic acid (SA) in aqueous solution. The value of 69 nm was selected as the optimal Δλ conditions for Phe and 1H2NA, and the Δλ value of 55 nm was selected for SA. The overlapping fluorescence emission spectra of Phe, 1H2NA and SA were resolved by DS-DSFS. The signals detected at wavelength of 296 nm for Phe, 352 nm for 1H2NA and 307 nm for SA vary linearly when the concentrations in the range of 4.0-1.0 × 103 μg L-1, 4.0-1.2 × 103 μg L-1 and 4.0-8.0 × 102 μg L-1, respectively. The detection limits were 0.08, 0.07 and 0.88 μg L-1 for Phe, 1H2NA and SA, with the relatively standard deviations less than 5.0%. The established method was successfully applied in the determination of Phe and the metabolites during the biodegradation of dissolved Phe in the lab. It was evidenced that the method has potential for the in situ investigation of PAH biodegradation.
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Affiliation(s)
- Chaoxian Wei
- State Key Laboratory of Marine Environmental Science of China (Xiamen University), College of the Environment & Ecology, Xiamen University, 361102 Xiamen, Fujian Province, PR China
| | - Pei Ren
- State Key Laboratory of Marine Environmental Science of China (Xiamen University), College of the Environment & Ecology, Xiamen University, 361102 Xiamen, Fujian Province, PR China
| | - Qiulin Cen
- State Key Laboratory of Marine Environmental Science of China (Xiamen University), College of the Environment & Ecology, Xiamen University, 361102 Xiamen, Fujian Province, PR China
| | - Yaxian Zhu
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yong Zhang
- State Key Laboratory of Marine Environmental Science of China (Xiamen University), College of the Environment & Ecology, Xiamen University, 361102 Xiamen, Fujian Province, PR China.
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Sun S, Wang H, Chen Y, Lou J, Wu L, Xu J. Salicylate and phthalate pathways contributed differently on phenanthrene and pyrene degradations in Mycobacterium sp. WY10. JOURNAL OF HAZARDOUS MATERIALS 2019; 364:509-518. [PMID: 30388634 DOI: 10.1016/j.jhazmat.2018.10.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/11/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Mycobacterium sp. WY10 was a highly effective PAHs-degrading bacterium that can degrade phenanthrene (PHE, 100 mg L-1) completely within 60 h and 83% of pyrene (PYR, 50 mg L-1) in 72 h. In this study, ten and eleven metabolites, respectively, were identified in PHE and PYR degradation cultures, and a detailed PHE and PYR metabolism maps were constructed based on the metabolic results. The strain WY10 degraded PHE and PYR with initial dioxygenation mainly on 3,4- and 4,5-carbon positions, respectively. Thereafter, PYR degradation entered the PHE degradation pathway via the ortho-cleavage. It was observed that the "lower pathway" of PHE and PYR degradations were different. Based on the kinetics of residual metabolites, PHE was degraded in a dominant phthalate pathway and a minor salicylate pathway. However, both phthalate and salicylate pathways played important roles on PYR degradation. The WY10 genome revealed there were fifty-three genes related to PAHs degradations, including a complete gene set for PHE and PYR degradation via the phthalate pathway. The candidate gene/ORF, BOH72_19755, encoding salicylate synthase might contribute in the salicylate pathway.
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Affiliation(s)
- Shanshan Sun
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanzhi Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jun Lou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
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Ge Z, Wei D, Zhang J, Hu J, Liu Z, Li R. Natural pyrite to enhance simultaneous long-term nitrogen and phosphorus removal in constructed wetland: Three years of pilot study. WATER RESEARCH 2019; 148:153-161. [PMID: 30359945 DOI: 10.1016/j.watres.2018.10.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 10/12/2018] [Accepted: 10/13/2018] [Indexed: 06/08/2023]
Abstract
The searches for suitable substrates with high capacity for phosphorus (P) removal and promoting denitrification for enhancing nitrogen (N) removal have been a key work in constructed wetlands (CWs) research in the past several decades. But few substrates enhancing simultaneous long-term N and P removal in CWs have been found before. In this study, two subsurface flow pilot-scale wetlands using natural pyrite and limestone as substrates were constructed. After 3 year of operation, we found that pyrite had no negative effects on growth of reeds, removals of chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N), but enhanced long-term total nitrogen (TN) and total phosphorus (TP) removals in constructed wetland. In the three years, the average TP and TN removals of pyrite constructed wetland (PCW) were 87.7 ± 14.2% with 0.25 ± 0.20 mg/L of average effluent TP and 69.4 ± 21.4% with 4.0 ± 3.2 mg/L of average effluent TN, respectively. The main P form in the PCW was (Fe + Al)-bound P. The mechanisms of the PCW with enhanced simultaneous long-term N and P removals were anaerobic and aerobic oxidations of pyrite. The main bacteria were Anaeromyxobacter (4.9%), Ramlibacter (4.8%), Defluviicoccus (4.2%), Azoarcus (3.7%), Geobacter (3.4%), and they were highly related to anaerobic and aerobic oxidation of pyrite in the PCW.
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Affiliation(s)
- Zhibin Ge
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Ave., Nanjing, Jiangsu 210023, PR China
| | - Dongyang Wei
- South China Institute of Environmental Sciences, MEP, Guangzhou 510655, China
| | - Jing Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Ave., Nanjing, Jiangsu 210023, PR China
| | - Junsong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Ave., Nanjing, Jiangsu 210023, PR China
| | - Zhuo Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Ave., Nanjing, Jiangsu 210023, PR China
| | - Ruihua Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Ave., Nanjing, Jiangsu 210023, PR China.
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Wu H, Shen J, Jiang X, Liu X, Sun X, Li J, Han W, Mu Y, Wang L. Bioaugmentation potential of a newly isolated strain Sphingomonas sp. NJUST37 for the treatment of wastewater containing highly toxic and recalcitrant tricyclazole. BIORESOURCE TECHNOLOGY 2018; 264:98-105. [PMID: 29793119 DOI: 10.1016/j.biortech.2018.05.071] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
In order to develop an effective bioaugmentation strategy for the removal of highly toxic and recalcitrant tricyclazole from wastewater, a tricyclazole degrading strain was firstly successfully isolated and identified as Sphingomonas sp. NJUST37. In batch reactors, 100 mg L-1 tricyclazole could be completely removed within 102 h, which was accompanied by significant biomass increase, TOC and COD removal, as well as toxicity reduction. Chromatography analysis and density functional theory simulation indicated that monooxygenation occurred firstly, followed by triazole ring cleavage, decyanation reaction, hydration reaction, deamination, dihydroxylation and final mineralization reaction. Tricyclazole biodegradation condition by NJUST37 was optimized in terms of temperature, pH, tricyclazole concentration and additional carbon and nitrogen sources. After the inoculation of NJUST37 into a pilot-scale powdered activated carbon treatment tank treating real fungicide wastewater, tricyclazole removal efficiency increased to higher than 90%, demonstrating the great potential of NJUST37 for bioaugmentation particularly on tricyclazole biodegradation in practice.
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Affiliation(s)
- Haobo Wu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jinyou Shen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xinbai Jiang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xiaodong Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xiuyun Sun
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jiansheng Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Weiqing Han
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Lianjun Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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Fu W, Xu M, Sun K, Hu L, Cao W, Dai C, Jia Y. Biodegradation of phenanthrene by endophytic fungus Phomopsis liquidambari in vitro and in vivo. CHEMOSPHERE 2018; 203:160-169. [PMID: 29614409 DOI: 10.1016/j.chemosphere.2018.03.164] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 03/03/2018] [Accepted: 03/24/2018] [Indexed: 06/08/2023]
Abstract
Phenanthrene, as a widespread polycyclic aromatic hydrocarbons (PAHs) contaminant in vitro and in vivo of plant, has the characteristics of carcinogenicity, teratogenicity and mutagenicity. This work aimed to explore the phenanthrene metabolic mechanism by Phomopsis liquidambari in vitro, as well as the bioremediation ability through P. liquidambari-rice combination. This strain was able to use phenanthrene as source of carbon and energy to grow, more than 77% of added 50 mg L-1 phenanthrene was removed after 10 d in MSM. We identified the metabolic products via HPLC-MS and proposed two possible degradation pathways. Phenanthrene was firstly combined with oxygen to become phenanthrene 9,10-oxide, and then degraded to 9-phenanthrol, followed by oxidization to 9,10-dihydroxyphenanthrene. In addition, that epoxide (phenanthrene 9,10-oxide) was also hydrolyzed to phenanthrene trans-9,10-dihydrodiol, and then dehydrogenized to 9,10-dihydroxyphenanthrene, which was further degraded to 9,10-phenanthrenequinone; during this metabolic pathway, the changes of P450 monooxygenase, epoxide hydrolase, dehydrogenase and catechol 2,3-dioxygenase activities and their corresponding gene transcription levels were closely related. What's more, P. liquidambari could combine with rice to eliminate phenanthrene accumulated in vivo of rice seedlings, and the removal rate in inoculation treatment represented a significant difference (increased 25.68%) compared with uninoculation treatment after cultivation 30 d. Therefore, we concluded that P. liquidambari could not only respond to phenanthrene pollution stress in vitro but also exert a mitigation effect on plants accumulated phenanthrene. This work provides a foundation for applying endophytic fungi to PAHs bioremediation in vitro and in vivo.
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Affiliation(s)
- Wanqiu Fu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Man Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Liyan Hu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei Cao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Singleton DR, Lee J, Dickey AN, Stroud A, Scholl EH, Wright FA, Aitken MD. Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov. Syst Appl Microbiol 2018; 41:460-472. [PMID: 29937052 DOI: 10.1016/j.syapm.2018.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C16:1ω7c/C16:1ω6c, C16:0, and C18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3T as the type strain (=LMG 30136, =DSM 105008).
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Affiliation(s)
- David R Singleton
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA.
| | - Janice Lee
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Aaron Stroud
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
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Xu XH, Liu XM, Zhang L, Mu Y, Zhu XY, Fang JY, Li SP, Jiang JD. Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community. JOURNAL OF HAZARDOUS MATERIALS 2018; 351:240-249. [PMID: 29550558 DOI: 10.1016/j.jhazmat.2018.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/02/2018] [Accepted: 03/03/2018] [Indexed: 05/24/2023]
Abstract
Although bioaugmentation of pollutant-contaminated sites is a great concern, there are few reports on the relationships among indigenous microbial consortia, exogenous inocula, and pollutants in a bioaugmentation process. In this study, bioaugmentation with Pseudochrobactrum sp. BSQ1 and Massilia sp. BLM18, which can hydrolytically and reductively dehalogenate chlorothalonil (TPN), respectively, was studied for its ability to remove TPN from soil; the alteration of the soil microbial community during the bioaugmentation process was investigated. The results showed that TPN (50 mg/kg) was completely removed in both bioaugmentation treatments within 35 days with half-lives of 6.8 and 9.8 days for strains BSQ1 and BLM18 respectively. In high concentration of TPN-treated soils (100 mg/kg), the bioaugmentation with strains BSQ1 and BLM18 respectively reduced 76.7% and 62.0% of TPN within 35 days. The TPN treatment significantly decreased bacterial richness and diversity and improved the growth of bacteria related to the elimination of chlorinated organic pollutants. However, little influence on soil microbial community was observed for each inoculation treatment (without TPN treatment), showing that TPN treatment is the main force for the shift in indigenous consortia. This study provides insights into the effects of halogenated fungicide application and bioaugmentation on indigenous soil microbiomes.
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Affiliation(s)
- Xi-Hui Xu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiao-Mei Liu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018, Hohhot, China
| | - Long Zhang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yang Mu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xu-Yuan Zhu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jing-Ya Fang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shun-Peng Li
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; Jiangsu Key Lab for Solid Organic Waste Utilization, 210095, Nanjing, China.
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Lou J, Yang L, Wang H, Wu L, Xu J. Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification. PeerJ 2018; 6:e4514. [PMID: 29576979 PMCID: PMC5857175 DOI: 10.7717/peerj.4514] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/26/2018] [Indexed: 01/21/2023] Open
Abstract
Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.
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Affiliation(s)
- Jun Lou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Li Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,Department of Environmental Sciences, University of California, Riverside, United States of America
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
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Gu H, Chen Y, Liu X, Wang H, Shen-Tu J, Wu L, Zeng L, Xu J. The effective migration of Massilia sp. WF1 by Phanerochaete chrysosporium and its phenanthrene biodegradation in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:695-703. [PMID: 28363181 DOI: 10.1016/j.scitotenv.2017.03.205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Pollutant-degrading bacteria migrated by fungi may enhance the contacts between microorganisms and pollutants and improve the bioremediation efficiency of persistent organic pollutants in soil. Here, the migration of phenanthrene (PHE)-degrading bacteria Massilia sp. WF1 and Mycobacterium sp. WY10 by the hydrophobic fungi Phanerochaete chrysosporium (P. chrysosporium) and its effects on the PHE biodegradation in soil were investigated. Migration of the hydrophilic bacterium WF1 was better than that of the hydrophobic bacterium WY10 by P. chrysosporium mycelia since strain WF1 possesses flagellum and the type III secretion system. The interaction energy change of P. chrysosporium-WF1 was lower, but the interaction forces (van der Waals attractions, capillary forces, and cross-linking effects) were stronger than those of P. chrysosporium-WY10. Thus, the adhesive attraction between strain WF1 and P. chrysosporium was stronger, and consequently, strain WF1 was migrated by P. chrysosporium to a greater extent than WY10. The corresponding migration mechanism was inferred to be a bacterial 'passive' method: bacteria adhered to mycelia before they migrated with the growing mycelia. Moreover, migrated strain WF1 via P. chrysosporium showed effective PHE biodegradation in soil. Fungus-mediated migration of pollutant-degrading bacteria may play an important role in the bioremediation of pollutants in soil.
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Affiliation(s)
- Haiping Gu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Department of Environmental Sciences, College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuanzhi Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Xingmei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Jue Shen-Tu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Laosheng Wu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Lingzao Zeng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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Lu H, Sun J, Zhu L. The role of artificial root exudate components in facilitating the degradation of pyrene in soil. Sci Rep 2017; 7:7130. [PMID: 28769098 PMCID: PMC5541004 DOI: 10.1038/s41598-017-07413-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/26/2017] [Indexed: 11/09/2022] Open
Abstract
Root exudates play an important role in the phytoremediation of soils contaminated by organic pollutants, but how root exudate components affect the remediation process is not well understood. In this study, we explored the effects and mechanisms of the major root exudates, including glucose, organic acids, and serine, in the rhizoremediation of pyrene-contaminated soil. The results showed that glucose increased the degradation of pyrene (54.3 ± 1.7%) most significantly compared to the organic acids (45.5 ± 2.5%) and serine (43.2 ± 0.1%). Glucose could significantly facilitate the removal of pyrene in soil through promoting dehydrogenase activity indicated by a positive correlation between the removal efficiency of pyrene and the soil dehydrogenase activity (p < 0.01). Furthermore, root exudates were able to change soil microbial community, particularly the bacterial taxonomic composition, thereby affecting the biodegradation of pyrene. Glucose could alter soil microbial community and enhance the amount of Mycobacterium markedly, which is dominant in the degradation of pyrene. These findings provide insights into the mechanisms by which root exudates enhance the degradation of organic contaminants and advance our understanding of the micro-processes involved in rhizoremediation.
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Affiliation(s)
- Hainan Lu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Jianteng Sun
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China.
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