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Wang Q, Hou J, Huang Y, Liu W, Christie P. Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166759. [PMID: 37659531 DOI: 10.1016/j.scitotenv.2023.166759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L-1 pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.
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Affiliation(s)
- Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ya Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Iriarte J, Dachs J, Casas G, Martínez-Varela A, Berrojalbiz N, Vila-Costa M. Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1625-1636. [PMID: 36655903 PMCID: PMC9893724 DOI: 10.1021/acs.est.2c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 05/28/2023]
Abstract
The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.
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Cazals F, Colombano S, Huguenot D, Betelu S, Galopin N, Perrault A, Simonnot MO, Ignatiadis I, Rossano S, Crampon M. Polycyclic aromatic hydrocarbons remobilization from contaminated porous media by (bio)surfactants washing. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 251:104065. [PMID: 36054960 DOI: 10.1016/j.jconhyd.2022.104065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 08/01/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Biosurfactants, surface-active agents produced by microorganisms, are increasingly studied for their potential use in soil remediation processes because they are more environmentally friendly than their chemically produced homologues. In this work, we report on the use of a crude biosurfactant produced by a bacterial consortium isolated from a PAHs-contaminated soil, compared with other (bio)surfactants (Tween80, Sodium dodecyl sulfate - SDS, rhamnolipids mix), to wash PAHs from a contaminated porous media. Assays were done using columns filled with sand or sand-clay mixtures (95:5) spiked with four model PAHs. The crude biosurfactant showed less adsorption to the [sand] and the [sand + clay] columns compared to Tween 80, SDS and the rhamnolipid mix. The biosurfactant showed the second best capacity to remove PAHs from the columns (as dissolved and particulate phases), both from [sand] and [sand + clay], after SDS when applied at lower concentrations than the other sufactants. The effluent concentrations of phenanthrene (PHE), pyrene (PYR) and benzo[a]pyrene (BAP) increased in the presence of the crude biosurfactant. Compared to the control experiment using only water, the global PAHs washed mass (amount of PAHs removed from the columns) increased between 9 and 1000 times for PHE and BAP in the [sand] column, and between 55 and 6000 times respectively for PHE and BAP in the [sand + clay] columns. Moreover, in the [sand + clay] columns, leaching of a part of the clays was observed in the SDS and the biosurfactant injections assays. This clay leaching resulted in higher PAHs removal, due not to desorption but rather to particulate transport. In the context of washing PAH-contaminated soils in biopiles or subsurface remediation, our results could help in sizing the remediation approach using an environmental friendly biosurfactant, before a pump-and-treat process.
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Affiliation(s)
- Florian Cazals
- Laboratoire Géomatériaux et Environnement, Université Paris-Est Marne-la-Vallée, France; Colas Environnement, France; Bureau de Recherches Géologiques et Minières (BRGM), F-45060 Orléans, France.
| | - Stéfan Colombano
- Bureau de Recherches Géologiques et Minières (BRGM), F-45060 Orléans, France.
| | - David Huguenot
- Laboratoire Géomatériaux et Environnement, Université Paris-Est Marne-la-Vallée, France.
| | - Stéphanie Betelu
- Bureau de Recherches Géologiques et Minières (BRGM), F-45060 Orléans, France.
| | | | | | | | - Ioannis Ignatiadis
- Bureau de Recherches Géologiques et Minières (BRGM), F-45060 Orléans, France.
| | - Stéphanie Rossano
- Laboratoire Géomatériaux et Environnement, Université Paris-Est Marne-la-Vallée, France.
| | - Marc Crampon
- Bureau de Recherches Géologiques et Minières (BRGM), F-45060 Orléans, France.
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Li M, Xu M, Su A, Zhang Y, Niu L, Xu Y. Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome. Front Microbiol 2022; 13:888086. [PMID: 35602076 PMCID: PMC9114715 DOI: 10.3389/fmicb.2022.888086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.
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Affiliation(s)
- Mingyue Li
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Minmin Xu
- Shandong Academy of Environmental Sciences Co., Ltd., Jinan, China
| | - Aoxue Su
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Ying Zhang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Lili Niu
- Key Laboratory of Pollution Exposure and Health Intervention Technology, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, China
| | - Yan Xu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
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Halfadji A, Portet-Koltalo F, Touabet A, Le Derf F, Morin C, Merlet-Machour N. Phytoremediation of PCB: contaminated Algerian soils using native agronomics plants. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:117-132. [PMID: 34355306 DOI: 10.1007/s10653-021-01049-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Pot cultivation experiments were conducted to assess the phytoremediation potential of two local agronomic plants, namely Avena sativa and Vicia sativa. Several soils with long-standing contamination and different levels of Polychlorinated biphenyl (PCB) contamination were used for this study. The soil samples came from different regions of Algeria and had different physico-chemical parameters. We studied the influence of these parameters on remediation potential of the two tested plants. The removal rate of the seven PCBs (PCB 28, 52, 101, 138, 153, 156 and 180) was examined after 40 and 90 days. The results showed that the presence of the plants reduced significantly the overall PCB content, ranging initially from 1.33-127.9 mg kg1. After 90 days, the forage plant Vicia sativa allowed us to reach an excess dissipation rate of 56.7% compared to the unplanted control for the most polluted soil. An average dissipation rate of 50% was obtained in the moderately polluted soil. The less contaminated soil had an excess dissipation rate of about 24% for both plants and a predominant dissipation of the low chlorinated PCBs.
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Affiliation(s)
- Ahmed Halfadji
- Department of Sciences and Technology, Faculty of Applied Science, University Ibn-Khaldoun Tiaret, BP 78 P zaâroura 14000, Tiaret, Algeria
- UNIROUEN, Laboratory of Organic and Bioorganic Chemistry, Reactivity and Analysis COBRA UMR CNRS 6014, IUT Evreux, 55 rue St Germain, 27000, Evreux, France
- Laboratory of Organic Analysis Functional (LAOF), Faculty of Chemistry, University of Sciences and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Florence Portet-Koltalo
- UNIROUEN, Laboratory of Organic and Bioorganic Chemistry, Reactivity and Analysis COBRA UMR CNRS 6014, IUT Evreux, 55 rue St Germain, 27000, Evreux, France
| | - Abdelkrim Touabet
- Department of Sciences and Technology, Faculty of Applied Science, University Ibn-Khaldoun Tiaret, BP 78 P zaâroura 14000, Tiaret, Algeria
| | - Franck Le Derf
- UNIROUEN, Laboratory of Organic and Bioorganic Chemistry, Reactivity and Analysis COBRA UMR CNRS 6014, IUT Evreux, 55 rue St Germain, 27000, Evreux, France
| | - Christophe Morin
- UNIROUEN, Laboratory of Organic and Bioorganic Chemistry, Reactivity and Analysis COBRA UMR CNRS 6014, IUT Evreux, 55 rue St Germain, 27000, Evreux, France
| | - Nadine Merlet-Machour
- UNIROUEN, Laboratory of Organic and Bioorganic Chemistry, Reactivity and Analysis COBRA UMR CNRS 6014, IUT Evreux, 55 rue St Germain, 27000, Evreux, France.
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Liu XX, Hu X, Cao Y, Pang WJ, Huang JY, Guo P, Huang L. Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-Tolerant Burkholderia fungorum FM-2. Front Microbiol 2019; 10:408. [PMID: 30930861 PMCID: PMC6427951 DOI: 10.3389/fmicb.2019.00408] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L−1, respectively, while the MIC of Zn(II) was >1,200 mg L−1. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L−1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.
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Affiliation(s)
- Xin-Xin Liu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Xin Hu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Yue Cao
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Wen-Jing Pang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Jin-Yu Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Peng Guo
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
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Evaluating the mycostimulation potential of select carbon amendments for the degradation of a model PAH by an ascomycete strain enriched from a superfund site. Biodegradation 2018; 29:463-471. [PMID: 30003496 DOI: 10.1007/s10532-018-9843-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/29/2018] [Indexed: 12/23/2022]
Abstract
Although ecological flexibility has been well documented in fungi, it remains unclear how this flexibility can be exploited for pollutant degradation, especially in the Ascomycota phylum. In this work, we assess three mycostimulation amendments for their ability to induce degradation in Trichoderma harzanium, a model fungus previously isolated from a Superfund site contaminated with polycyclic aromatic hydrocarbons. The amendments used in the present study were selected based on the documented ecological roles of ascomycetes. Chitin was selected to simulate the parasitic ecological role while cellulose and wood were selected to mimic bulk soil and wood saprobic conditions, respectively. Each amendment was tested in liquid basal medium in 0.1 and 1% (w/v) suspensions. Both chitin and cellulose amendments were shown to promote anthracene degradation in T. harzanium with the 0.1% chitin amendment resulting in over 90% removal of anthracene. None of the targets monitored for gene expression were found to be upregulated suggesting alternate pathways may be used in T. harzanium. Overall, our data suggest that mycostimulation amendments can be improved by understanding the ecological roles of indigenous fungi. However, further research is needed to better estimate specific amendment requirements for a broader group of target fungi and follow up studies are needed to determine whether the trends observed herein translate to more realistic soil systems.
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Roslund MI, Grönroos M, Rantalainen AL, Jumpponen A, Romantschuk M, Parajuli A, Hyöty H, Laitinen O, Sinkkonen A. Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials. PeerJ 2018; 6:e4508. [PMID: 29576975 PMCID: PMC5863720 DOI: 10.7717/peerj.4508] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/26/2018] [Indexed: 12/13/2022] Open
Abstract
Background Polycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial. Methods Four landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 µg g -1 soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding. Results Half-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1–2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria. Conclusions In this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.
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Affiliation(s)
- Marja I Roslund
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Mira Grönroos
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Anna-Lea Rantalainen
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Kansas, Manhattan, United States of America
| | - Martin Romantschuk
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Anirudra Parajuli
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Olli Laitinen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Aki Sinkkonen
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
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Mukhopadhyay S, George J, Masto RE. Changes in Polycyclic Aromatic Hydrocarbons (PAHs) and Soil Biological Parameters in a Revegetated Coal Mine Spoil. LAND DEGRADATION & DEVELOPMENT 2017; 28:1047-1055. [PMID: 0 DOI: 10.1002/ldr.2593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Sangeeta Mukhopadhyay
- Environmental Management DivisionCSIR—Central Institute of Mining and Fuel Research (Digwadih Campus) Dhanbad 828108 India
| | - Joshy George
- Environmental Management DivisionCSIR—Central Institute of Mining and Fuel Research (Digwadih Campus) Dhanbad 828108 India
| | - Reginald E. Masto
- Environmental Management DivisionCSIR—Central Institute of Mining and Fuel Research (Digwadih Campus) Dhanbad 828108 India
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