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K S, Manian R. Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1441. [PMID: 37946088 DOI: 10.1007/s10661-023-12042-7] [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: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.
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Affiliation(s)
- Sumathi K
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rameshpathy Manian
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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Liang C, Ye Q, Huang Y, Wang Y, Zhang Z, Wang H. Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129305. [PMID: 35709619 DOI: 10.1016/j.jhazmat.2022.129305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/22/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R2 = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.
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Affiliation(s)
- Chengyue Liang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Ibrahim MM, Guo L, Wu F, Liu D, Zhang H, Zou S, Xing S, Mao Y. Field-applied biochar-based MgO and sepiolite composites possess CO 2 capture potential and alter organic C mineralization and C-cycling bacterial structure in fertilized soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152495. [PMID: 34968614 DOI: 10.1016/j.scitotenv.2021.152495] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Agricultural soils contribute a significant amount of anthropogenic CO2 emission, a greenhouse gas of global environmental concern. Hence, discovering sustainable materials that can capture CO2 in cultivated soils is paramount. Since the effect of biochar on C mineralization/retention in fertilized soils is unclear, we produced biochar-based MgO and sepiolite-nanocomposites with CO2 capture potential. The field-scale impacts of the modified-biochars were evaluated on net C exchange rate (NCER) periodically for 3 months in fertilized plots. The effects of the modified-biochar on organic-C mineralization, the activities, and dynamics of C-cycling-related 16S rRNA which are unknown, were investigated. Results revealed an initial rapid and higher cumulative CO2 emission from the sole fertilizer treatment (F). Unlike the biochar treatment (BF), the successful incorporation of MgO/Mg(OH)2 nanoparticles into the matrix and surface of biochar, and the potential formation of MgCO3 with soil CO2, mitigated CO2 emission, especially in the MgO-modified biochar (MgOBF), compared to the sepiolite-biochar treatment (SBF). Compared to F and BF, the higher C retention as MgCO3 in the modified biochar treatments led to an increase in cellulase activity, stimulation of key C-cycling-related bacteria, and the expression of genes associated with starch, sucrose, amino sugar, nucleotide sugar, ascorbate, aldarate, cellulose, and chitin degradation, thus, increasing organic C mineralization. Among the modified-biochar treatments, higher C mineralization was recorded in SBF, resulting in increased cumulative CO2 emission, despite its initial capture for up to 42 days. However, MgOBF was effective in capturing soil-derived CO2, despite the increased C mineralization compared to biochar. The changes in soil moisture and temperature significantly regulated NCER. Also, the modified biochars positively influenced the distribution of C-cycling-related bacteria by improving soil pH and available nutrients. Among the modified biochars, the observed higher mitigation effect of MgOBF on NCER indicated that it could be preferably applied in agricultural soils.
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Affiliation(s)
- Muhammed Mustapha Ibrahim
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China; Department of Soil Science, Joseph Sarwuan Tarka University, P.M.B, 2373 Makurdi, Nigeria
| | - Liming Guo
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Fengying Wu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Dongming Liu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Hongxue Zhang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Shuangquan Zou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Shihe Xing
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Yanling Mao
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China.
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Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
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Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
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5
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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Li J, He J, Niu Z, Zhang Y. Legacy per- and polyfluoroalkyl substances (PFASs) and alternatives (short-chain analogues, F-53B, GenX and FC-98) in residential soils of China: Present implications of replacing legacy PFASs. ENVIRONMENT INTERNATIONAL 2020; 135:105419. [PMID: 31874352 DOI: 10.1016/j.envint.2019.105419] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 05/27/2023]
Abstract
With the worldwide regulation of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), the alternatives (short chain analogues and emerging per- and polyfluoroalkyl substances, PFASs) have gradually attracted global attention. This study analysed the replacing of legacy PFASs in China using PFASs data from residential soils, which might be good environmental indicators of their present usage. The total concentrations of 21 PFASs ranged from 244 to 13564 pg/g, and PFOA was the dominant compound among the studied PFASs, with a concentration of 354 ± 439 pg/g. Serious PFASs pollution in residential soils mainly occurred in Eastern Coastal China as a result of locally developed industry and economies. Weak but significant correlations were found between PFASs and environmental and socioeconomic factors, suggesting that various factors determine PFASs contamination in residential soils. The concentration and detection frequency (DF) of short-chain analogues (C < 8) (375 ± 509 pg/g and 100%), and F-53B (216 ± 306 pg/g and 98.9%) were higher than those for PFOS (193 ± 502 pg/g and 85.4%), indicating that these compounds have been widely used as PFOS alternatives and their consumption has already exceeded that of PFOS in China. In addition, GenX (the PFOA alternative) had a concentration and DF of 19.1 ± 104 pg/g and 40.5%, respectively. These values were much lower than those for PFOA (354 ± 439 pg/g and 96.6%), indicating GenX consumption is still limited at the national scale of China, despite its use as a PFOA replacement. Moreover, the low concentration and DF of FC-98 (2.31 ± 11.1 pg/g and 27.0%) indicate that its consumption might be negligible. Our study demonstrated that short chain analogues and emerging alternatives have become the dominant PFAS pollutants in Chinese residential soils, and further studies need to be conducted to understand their toxicity and environmental risks.
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Affiliation(s)
- Jiafu Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiahui He
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhiguang Niu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Ying Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Lu C, Hong Y, Liu J, Gao Y, Ma Z, Yang B, Ling W, Waigi MG. A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:773-782. [PMID: 31121542 DOI: 10.1016/j.envpol.2019.05.044] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/21/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.
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Affiliation(s)
- Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Hong
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Haleyur N, Shahsavari E, Jain SS, Koshlaf E, Ravindran VB, Morrison PD, Osborn AM, Ball AS. Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 238:49-58. [PMID: 30844545 DOI: 10.1016/j.jenvman.2019.02.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.
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Affiliation(s)
- Nagalakshmi Haleyur
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
| | - Esmaeil Shahsavari
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Sohni Singh Jain
- Department of Electrical and Biomedical Engineering, School of Engineering, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Eman Koshlaf
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Paul D Morrison
- Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - A Mark Osborn
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
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Sivaram AK, Logeshwaran P, Lockington R, Naidu R, Megharaj M. Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria. CHEMOSPHERE 2019; 222:132-140. [PMID: 30703652 DOI: 10.1016/j.chemosphere.2019.01.110] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The biodegradation potential of three bacterial cultures isolated from the rhizosphere of maize (Zea mays) and Sudan grass (Sorghum sudanense) grown in PAHs contaminated soils to degrade benzo[a]pyrene (BaP) and pyrene (PYR) was assessed. Of the three bacterial cultures isolated, two belonged to Gram-positive bacteria of phylum Actinobacteria namely Arthrobacter sp. MAL3 and Microbacterium sp. MAL2. The Gram-negative bacterial culture was Stenotrophomonas sp. MAL1, from the phylum Proteobacteria. The cultures were grown in the presence of BaP and PYR as sole carbon sources and with the addition of low molecular weight organic acids (LMWOAs) mixture. After 10-14 days of exposure, all the bacterial isolates exhibited a complete degradation of PYR with the addition of LMWOAs mixture, whereas only 38.7% of BaP was degraded by Stenotrophomonas sp. MAL1 with the addition of LMWOAs mixture. In addition, enhanced PAHs biodegradation by bacterial culture was observed when the PAHs present as mixture (BaP + PYR) with the addition of LMWOAs. Dioxygenase genes were detected in Stenotrophomonas sp. MAL1 (phnAC), and Arthrobacter sp. MAL3 (nidA and PAH-RHDα). Therefore, this study provides new insights on the influence of LMWOAs in enhancing the degradation of high molecular weight (HMW) PAHs in soil by rhizosphere bacterial cultures.
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Affiliation(s)
- Anithadevi Kenday Sivaram
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle (UoN), University Drive, Callaghan, NSW, 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Panneerselvan Logeshwaran
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle (UoN), University Drive, Callaghan, NSW, 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Robin Lockington
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle (UoN), University Drive, Callaghan, NSW, 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle (UoN), University Drive, Callaghan, NSW, 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.
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Fanesi A, Zegeye A, Mustin C, Cébron A. Soil Particles and Phenanthrene Interact in Defining the Metabolic Profile of Pseudomonas putida G7: A Vibrational Spectroscopy Approach. Front Microbiol 2018; 9:2999. [PMID: 30564224 PMCID: PMC6288191 DOI: 10.3389/fmicb.2018.02999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/20/2018] [Indexed: 01/21/2023] Open
Abstract
In soil, organic matter and mineral particles (soil particles; SPs) strongly influence the bio-available fraction of organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), and the metabolic activity of bacteria. However, the effect of SPs as well as comparative approaches to discriminate the metabolic responses to PAHs from those to simple carbon sources are seldom considered in mineralization experiments, limiting our knowledge concerning the dynamics of contaminants in soil. In this study, the metabolic profile of a model PAH-degrading bacterium, Pseudomonas putida G7, grown in the absence and presence of different SPs (i.e., sand, clays and humic acids), using either phenanthrene or glucose as the sole carbon and energy source, was characterized using vibrational spectroscopy (i.e., FT-Raman and FT-IR spectroscopy) and multivariate classification analysis (i.e., PLS-DA). The different type of SPs specifically altered the metabolic profile of P. putida, especially in combination with phenanthrene. In comparison to the cells grown in the absence of SPs, sand induced no remarkable change in the metabolic profile of the cells, whereas clays and humic acids affected it the most, as revealed by the higher discriminative accuracy (R2, RMSEP and sensitivity) of the PLS-DA for those conditions. With respect to the carbon-source (phenanthrene vs. glucose), no effect on the metabolic profile was evident in the absence of SPs or in the presence of sand. On the other hand, with clays and humic acids, more pronounced spectral clusters between cells grown on glucose or on phenanthrene were evident, suggesting that these SPs modify the way cells access and metabolize PAHs. The macromolecular changes regarded mainly protein secondary structures (a shift from α-helices to β-sheets), amino acid levels, nucleic acid conformation and cell wall carbohydrates. Our results provide new interesting evidences that SPs specifically interact with PAHs in defining bacteria metabolic profiles and further emphasize the importance of studying the interaction of bacteria with their surrounding matrix to deeply understand PAHs degradation in soils.
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Affiliation(s)
- Andrea Fanesi
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Asfaw Zegeye
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Christian Mustin
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Aurélie Cébron
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
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11
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Storey S, Ashaari MM, Clipson N, Doyle E, de Menezes AB. Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study. Front Microbiol 2018; 9:2815. [PMID: 30519226 PMCID: PMC6258822 DOI: 10.3389/fmicb.2018.02815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.
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Affiliation(s)
- Sean Storey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Mardiana Mohd Ashaari
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Malaysia, Malaysia
| | - Nicholas Clipson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Alexandre B de Menezes
- Microbiology, School of Natural Sciences, Ryan Institute, National University of Ireland, Galway, Ireland
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12
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Schwarz A, Adetutu EM, Juhasz AL, Aburto-Medina A, Ball AS, Shahsavari E. Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils. MICROBIAL ECOLOGY 2018; 75:888-902. [PMID: 29080101 DOI: 10.1007/s00248-017-1094-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/15/2017] [Indexed: 06/07/2023]
Abstract
Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event (14C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.
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Affiliation(s)
- Alexandra Schwarz
- Discipline of Biological Sciences, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Eric M Adetutu
- Medical Biotechnology, School of Medicine, Flinders University, Adelaide, Australia
| | - Albert L Juhasz
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia.
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13
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Roguet A, Therial C, Catherine A, Bressy A, Varrault G, Bouhdamane L, Tran V, Lemaire BJ, Vincon-Leite B, Saad M, Moulin L, Lucas FS. Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes. MICROBIAL ECOLOGY 2018; 75:834-846. [PMID: 29063147 DOI: 10.1007/s00248-017-1088-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 103 to 1.9 × 108 genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.
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Affiliation(s)
- Adélaïde Roguet
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France.
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
| | - Claire Therial
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005, Paris, France
| | - Adèle Bressy
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Gilles Varrault
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Lila Bouhdamane
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Viet Tran
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Bruno J Lemaire
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | | | - Mohamed Saad
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Laurent Moulin
- Eau de Paris, Direction Recherche et Développement Qualité de l'Eau (DRDQE), 33 avenue Jean Jaurès, FR 94200, Ivry-sur-Seine, France
| | - Françoise S Lucas
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
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14
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Hemkemeyer M, Dohrmann AB, Christensen BT, Tebbe CC. Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses. Front Microbiol 2018. [PMID: 29527192 PMCID: PMC5829042 DOI: 10.3389/fmicb.2018.00149] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs. The PSFs were obtained by gentle ultrasonic dispersion, wet sieving, and centrifugation. The abundance of bacterial taxa assigned to operational taxonomic units (OTUs) differed less than 2.7% between unfractionated soil and soil based on combined PSFs. Across the three soil variants, no archaeal OTUs, but many bacterial OTUs, the latter representing 34–56% of all amplicon sequences, showed significant preferences for specific PSFs. The sand-sized fraction with POM was the preferred site for members of Bacteroidetes and Alphaproteobacteria, while Gemmatimonadales preferred coarse silt, Actinobacteria and Nitrosospira fine silt, and Planctomycetales clay. Firmicutes were depleted in the sand-sized fraction. In contrast, archaea, which represented 0.8% of all 16S rRNA gene sequences, showed only little preference for specific PSFs. We conclude that differently sized soil particles represent distinct microenvironments that support specific bacterial taxa and that these preferences could strongly contribute to the spatial heterogeneity and bacterial diversity found in soils.
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Affiliation(s)
- Michael Hemkemeyer
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
| | - Anja B Dohrmann
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
| | | | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
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15
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Vincent Q, Auclerc A, Beguiristain T, Leyval C. Assessment of derelict soil quality: Abiotic, biotic and functional approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:990-1002. [PMID: 28946386 DOI: 10.1016/j.scitotenv.2017.09.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
The intensification and subsequent closing down of industrial activities during the last century has left behind large surfaces of derelict lands. Derelict soils have low fertility, can be contaminated, and many of them remain unused. However, with the increasing demand of soil surfaces, they might be considered as a resource, for example for non-food biomass production. The study of their physico-chemical properties and of their biodiversity and biological activity may provide indications for their potential re-use. The objective of our study was to investigate the quality of six derelict soils, considering abiotic, biotic, and functional parameters. We studied (i) the soil bacteria, fungi, meso- and macro-fauna and plant communities of six different derelict soils (two from coking plants, one from a settling pond, two constructed ones made from different substrates and remediated soil, and an inert waste storage one), and (ii) their decomposition function based on the decomposer trophic network, enzyme activities, mineralization activity, and organic pollutant degradation. Biodiversity levels in these soils were high, but all biotic parameters, except the mycorrhizal colonization level, discriminated them. Multivariate analysis showed that biotic parameters co-varied more with fertility proxies than with soil contamination parameters. Similarly, functional parameters significantly co-varied with abiotic parameters. Among functional parameters, macro-decomposer proportion, enzyme activity, average mineralization capacity, and microbial polycyclic aromatic hydrocarbon degraders were useful to discriminate the soils. We assessed their quality by combining abiotic, biotic, and functional parameters: the compost-amended constructed soil displayed the highest quality, while the settling pond soil and the contaminated constructed soil displayed the lowest. Although differences among the soils were highlighted, this study shows that derelict soils may provide a biodiversity ecosystem service and are functional for decomposition.
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Affiliation(s)
- Quentin Vincent
- Université de Lorraine, CNRS, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, Vandoeuvre-lès-Nancy, France; Université de Lorraine, INRA, Laboratoire Sols et Environnement (LSE), UMR 1120, Vandoeuvre-lès-Nancy, France
| | - Apolline Auclerc
- Université de Lorraine, INRA, Laboratoire Sols et Environnement (LSE), UMR 1120, Vandoeuvre-lès-Nancy, France
| | - Thierry Beguiristain
- Université de Lorraine, CNRS, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, Vandoeuvre-lès-Nancy, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, Vandoeuvre-lès-Nancy, France.
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16
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Yu L, Duan L, Naidu R, Semple KT. Abiotic factors controlling bioavailability and bioaccessibility of polycyclic aromatic hydrocarbons in soil: Putting together a bigger picture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1140-1153. [PMID: 28954375 DOI: 10.1016/j.scitotenv.2017.09.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
The bioavailability and bioaccessibility of polycyclic aromatic hydrocarbons (PAHs) in soil underpin the risk assessment of contaminated land with these contaminants. Despite a significant volume of research conducted in the past few decades, comprehensive understanding of the factors controlling the behaviour of soil PAHs and a set of descriptive soil parameters to explain variations in PAH bioavailability and bioaccessibility are still lacking. This review focuses on the role of source materials on bioavailability and bioaccessibility of soil PAHs, which is often overlooked, along with other abiotic factors including contaminant concentration and mixture, soil composition and properties, as well as environmental factors. It also takes into consideration the implications of different types of risk assessment (ecological and human health) on bioavailability and bioaccessibility of PAHs in soil. We recommend that future research should (1) account for the effects of source materials on bioavailability and bioaccessibility of soil PAHs; (2) adopt non-disruptive methods to analyse soil components controlling PAH sequestration; (3) integrate both natural organic matter (NOM) and xenobiotic organic matter (XOM) while evaluating the influences of soil organic matter (SOM) on the behaviour of PAHs; and (4) consider the dissimilar desorption scenarios in ecological risk assessment and human health risk assessment while assessing PAH bioavailability and bioaccessibility.
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Affiliation(s)
- Linbo Yu
- Global Centre for Environmental Remediation (GCER), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE Pty Ltd), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Luchun Duan
- Global Centre for Environmental Remediation (GCER), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE Pty Ltd), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE Pty Ltd), ATC Building, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Kirk T Semple
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
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Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation. 3 Biotech 2018; 8:118. [PMID: 29430379 PMCID: PMC5803133 DOI: 10.1007/s13205-018-1134-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.
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18
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Xiong B, Zhang Y, Hou Y, Arp HPH, Reid BJ, Cai C. Enhanced biodegradation of PAHs in historically contaminated soil by M. gilvum inoculated biochar. CHEMOSPHERE 2017; 182:316-324. [PMID: 28501571 DOI: 10.1016/j.chemosphere.2017.05.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/30/2017] [Accepted: 05/03/2017] [Indexed: 05/22/2023]
Abstract
The inoculation of rice straw biochar with PAH-degrading Mycobacterium gilvum (1.27 × 1011 ± 1.24 × 1010 cell g-1), and the subsequent amendment of this composite material to PAHs contaminated (677 mg kg-1) coke plant soil, was conducted in order to investigate if would enhance PAHs biodegradation in soils. The microbe-biochar composite showed superior degradation capacity for phenanthrene, fluoranthene and pyrene. Phenanthrene loss in the microbe-biochar composite, free cell alone and biochar alone treatments was, respectively, 62.6 ± 3.2%, 47.3 ± 4.1% and non-significant (P > 0.05); whereas for fluoranthene loss it was 52.1 ± 2.3%; non-significant (P > 0.05) and non-significant (P > 0.05); and for pyrene loss it was 62.1 ± 0.9%; 19.7 ± 6.5% and 13.5 ± 2.8%. It was hypothesized that the improved remediation was underpinned by i) biochar enhanced mass transfer of PAHs from the soil to the carbonaceous biochar "sink", and ii) the subsequent degradation of the PAHs by the immobilized M. gilvum. To test this mechanism, a surfactant (Brij 30; 20 mg g-1 soil), was added to impede PAHs mass transfer to biochar and sorption. The surfactant increased solution phase PAH concentrations and significantly (P < 0.05) reduced PAH degradation in the biochar immobilized M. gilvum treatments; indicating the enhanced degradation occurred between the immobilized M. gilvum and biochar sorbed PAHs.
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Affiliation(s)
- Bijing Xiong
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Youchi Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Yanwei Hou
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
| | - Hans Peter H Arp
- Norwegian Geotechnical Institute (NGI), P.O. Box 3930, Ullevål Stadion, N-0806 Oslo, Norway.
| | - Brian J Reid
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Chao Cai
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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19
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Chen P, Zhang L, Guo X, Dai X, Liu L, Xi L, Wang J, Song L, Wang Y, Zhu Y, Huang L, Huang Y. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge. Front Microbiol 2016; 7:1340. [PMID: 27621725 PMCID: PMC5002886 DOI: 10.3389/fmicb.2016.01340] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/15/2016] [Indexed: 02/01/2023] Open
Abstract
The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.
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Affiliation(s)
- Ping Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Xiaoxuan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Li Liu
- Information Network Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Lijun Xi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai Shanghai, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
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Sungthong R, van West P, Heyman F, Jensen DF, Ortega-Calvo JJ. Mobilization of Pollutant-Degrading Bacteria by Eukaryotic Zoospores. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:7633-7640. [PMID: 27286642 DOI: 10.1021/acs.est.6b00994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The controlled mobilization of pollutant-degrading bacteria has been identified as a promising strategy for improving bioremediation performance. We tested the hypothesis whether the mobilization of bacterial degraders may be achieved by the action of eukaryotic zoospores. We evaluated zoospores that are produced by the soil oomycete Pythium aphanidermatum as a biological vector, and, respectively, the polycyclic aromatic hydrocarbon (PAH)-degrading bacteria Mycobacterium gilvum VM552 and Pseudomonas putida G7, acting as representative nonflagellated and flagellated species. The mobilization assay was performed with a chemical-in-capillary method, in which zoospores mobilized bacterial cells only when they were exposed to a zoospore homing inducer (5% (v/v) ethanol), which caused the tactic response and settlement of zoospores. The mobilization was strongly linked to a lack of bacterial motility, because the nonflagellated cells from strain M. gilvum VM552 and slightly motile, stationary-phase cells from P. putida G7 were mobilized effectively, but the actively motile, exponentially grown cells of P. putida G7 were not mobilized. The computer-assisted analysis of cell motility in mixed suspensions showed that the swimming rate was enhanced by zoospores in stationary, but not in exponentially grown, cells of P. putida G7. It is hypothesized that the directional swimming of zoospores caused bacterial mobilization through the thrust force of their flagellar propulsion. Our results suggest that, by mobilizing pollutant-degrading bacteria, zoospores can act as ecological amplifiers for fungal and oomycete mycelial networks in soils, extending their potential in bioremediation scenarios.
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Affiliation(s)
- Rungroch Sungthong
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, Seville 41080, Spain
| | - Pieter van West
- Aberdeen Oomycete Laboratory, University of Aberdeen, Institute of Medical Sciences , Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Fredrik Heyman
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences , Uppsala 750 07, Sweden
| | - Dan Funck Jensen
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences , Uppsala 750 07, Sweden
| | - Jose Julio Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, Seville 41080, Spain
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Li W, Wang D, Hu F, Li H, Ma L, Xu L. Exogenous IAA treatment enhances phytoremediation of soil contaminated with phenanthrene by promoting soil enzyme activity and increasing microbial biomass. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:10656-10664. [PMID: 26884240 DOI: 10.1007/s11356-016-6170-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/22/2016] [Indexed: 05/22/2023]
Abstract
In this study, we aimed to confirm that indole-3-acetic acid promotes plant uptake of phenanthrene (PHE), stimulates the activity of soil enzymes or microflora, and thereby accelerates the dissipation of PHE in soil. Four treatments were evaluated: PHE-contaminated soil planted with (1) ryegrass (T0), (2) ryegrass and supplemented with 1 mg kg(-1) indole-3-acetic acid (IAA) (T1), (3) ryegrass and supplemented with 5 mg kg(-1) IAA (T5), and (4) ryegrass and supplemented with 10 mg kg(-1) IAA (T10). After 30 days, PHE concentrations were lower for all treatments and the removal rate was 70.19, 89.17, 91.26, and 97.07 % for T0, T1, T5, and T10, respectively. PHE was only detected in the roots and not in the shoots. IAA facilitated the accumulation of PHE in the roots, and plants subjected to the T10 treatment had the highest levels. Exogenous IAA stimulated soil peroxidase activity in a dose-dependent manner, whereas soil polyphenoloxidase activity was not significantly increased, except in T10. Soil microbial biomass also increased in response to IAA treatment, particularly in T10. Furthermore, phospholipid fatty acid analysis showed that IAA treatment increased microbial biomass and alleviated environmental stress. Gram-positive bacteria are largely responsible for polycyclic aromatic hydrocarbon degradation, and we found that the ratio of gram-positive to gram-negative bacteria in the soil significantly increased as the IAA concentrations increased (P < 0.05). Correlation analysis indicated that the increase in soil microbial biomass, enzyme activity, and plant uptake of PHE promotes removal of PHE from the soil.
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Affiliation(s)
- Weiming Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Nanjing Scientific Institute of Vegetables and Flowers, Nanjing, 210095, People's Republic of China
| | - Dongsheng Wang
- Nanjing Scientific Institute of Vegetables and Flowers, Nanjing, 210095, People's Republic of China
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Lili Ma
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, College of Geographical Science, Nanjing Normal University, Nanjing, 210095, People's Republic of China
| | - Li Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Zhou L, Li H, Zhang Y, Han S, Xu H. Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities. Braz J Microbiol 2016; 47:271-8. [PMID: 26991271 PMCID: PMC4874584 DOI: 10.1016/j.bjm.2016.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 08/17/2015] [Indexed: 11/18/2022] Open
Abstract
Members of the Sphingomonas genus are often isolated from petroleum-contaminated soils due to their unique abilities to degrade polycyclic aromatic hydrocarbons (PAHs), which are important for in situ bioremediation. In this study, a combined phenotypic and genotypic approach using streptomycin-containing medium and Sphingomonas-specific PCR was developed to isolate and identify culturable Sphingomonas strains present in petroleum-contaminated soils in the Shenfu wastewater irrigation zone. Of the 15 soil samples examined, 12 soils yielded yellow streptomycin-resistant colonies. The largest number of yellow colony-forming units (CFUs) could reach 105 CFUs g−1 soil. The number of yellow CFUs had a significant positive correlation (p < 0.05) with the ratio of PAHs to total petroleum hydrocarbons (TPH), indicating that Sphingomonas may play a key role in degrading the PAH fraction of the petroleum contaminants at this site. Sixty yellow colonies were selected randomly and analyzed by colony PCR using Sphingomonas-specific primers, out of which 48 isolates had PCR-positive signals. The 48 positive amplicons generated 8 distinct restriction fragment length polymorphism (RFLP) patterns, and 7 out of 8 phylotypes were identified as Sphingomonas by 16S rRNA gene sequencing of the representative strains. Within these 7 Sphingomonas strains, 6 strains were capable of using fluorene as the sole carbon source, while 2 strains were phenanthrene-degrading Sphingomonas. To the best of our knowledge, this is the first report to evaluate the relationship between PAHs contamination levels and culturable Sphingomonas in environmental samples.
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Affiliation(s)
- Lisha Zhou
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Hui Li
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China; State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.
| | - Ying Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Siqin Han
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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High mycobacterial diversity in recreational lakes. Antonie van Leeuwenhoek 2016; 109:619-31. [PMID: 26873594 DOI: 10.1007/s10482-016-0665-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
Abstract
Although nontuberculous mycobacteria (NTM) are natural inhabitants of freshwater ecosystems, few studies have focused on their distribution in these habitats. Thus, the knowledge about the abundance as well as the composition of NTM remains limited and patchy in these environments. In this context, a prospective study was performed to identify favourable habitats for mycobacteria in two recreational lakes. Mycobacterial density and diversity were measured using quantitative real-time PCR and the MiSeq Illumina platform. For both lakes, five compartments were investigated, i.e. water column, air-water interface, sediment, epilithon and epiphyton biofilms. Nontuberculous mycobacteria were detected in all compartments in large densities and displayed a remarkable diversity. NTM were dominated by fast-growing species. Lakes and compartments appeared to shape mycobacteria assemblage composition as well as their densities. In both lakes, some OTUs assigned to the species level were identified as related to known opportunistic pathogens.
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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river. Sci Rep 2015; 5:17284. [PMID: 26607034 PMCID: PMC4660315 DOI: 10.1038/srep17284] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023] Open
Abstract
The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1–3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.
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Cébron A, Beguiristain T, Bongoua-Devisme J, Denonfoux J, Faure P, Lorgeoux C, Ouvrard S, Parisot N, Peyret P, Leyval C. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13724-13738. [PMID: 25616383 DOI: 10.1007/s11356-015-4117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.
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Affiliation(s)
- Aurélie Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP 70239, 54506, Vandoeuvre-lès-Nancy Cedex, France,
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26
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Han XM, Liu YR, Zhang LM, He JZ. Insight into the Modulation of Dissolved Organic Matter on Microbial Remediation of PAH-Contaminated Soils. MICROBIAL ECOLOGY 2015; 70:400-410. [PMID: 25707714 DOI: 10.1007/s00248-015-0575-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
Microorganisms play a key role in degradation of polycyclic aromatic hydrocarbons (PAHs) in environments. Dissolved organic matter (DOM) can enhance microbial degradation of PAHs in soils. However, it is not clear how will the soil microbial community respond to addition of DOM during bioremediation of PAH-contaminated soils. In this study, DOMs derived from various agricultural wastes were applied to remediate the aging PAH-contaminated soils in a 90-day microcosm experiment. Results showed that the addition of DOMs offered a more efficient and persistent elimination of soil PAHs compared to the control which had no DOM addition. PAH removal effects were different among treatments with various DOMs; the addition of DOMs with high proportion of hydrophobic fraction could remove PAHs more efficiently from the soil. Low-molecular-weight (LMW) PAHs were more easily eliminated than that with high-molecular-weight (HMW). Addition of DOMs significantly increased abundance of 16S ribosomal RNA (rRNA), pdo1, nah, and C12O genes and obviously changed community compositions of nah and C12O genes in different ways in the PAH-contaminated soil. Phylogenetic analyses of clone libraries exhibited that all of nah sequences and most of C12O sequences were affiliated into Gammaproteobacteria and Betaproteobacteria. These results suggested that external stimuli produced by DOMs could enhance the microbial degradation of PAHs in soils through not only solubilizing PAHs but also altering abundance and composition of indigenous microbial degraders. Our results reinforce the understanding of role of DOMs in mediating degradation of PAHs by microorganims in soils.
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Affiliation(s)
- Xue-Mei Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
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27
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Sungthong R, van West P, Cantos M, Ortega-Calvo JJ. Development of eukaryotic zoospores within polycyclic aromatic hydrocarbon (PAH)-polluted environments: a set of behaviors that are relevant for bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 511:767-776. [PMID: 25617701 DOI: 10.1016/j.scitotenv.2014.12.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/26/2014] [Accepted: 12/26/2014] [Indexed: 06/04/2023]
Abstract
In this study, we assessed the development (formation, taxis and settlement) of eukaryotic zoospores under different regimes of exposure to polycyclic aromatic hydrocarbons (PAHs), which imitated environmental scenarios of pollution and bioremediation. With this aim, we used an oomycete, Pythium aphanidermatum, as a source of zoospores and two PAH-degrading bacteria (Mycobacterium gilvum VM552 and Pseudomonas putida G7). The oomycete and both bacteria were not antagonistic, and zoospore formation was diminished only in the presence of the highest bacterial cell density (10(8)-10(10) colony-forming units mL(-1)). A negative influence of PAHs on zoospore formation and taxis was observed when PAHs were exposed in combination with organic solutions and polar solvents. Co-exposure of PAHs with non-polar solvents [hexadecane (HD) and 2,2,4,4,6,8,8-heptamethylnonane (HMN)] did not affect zoospore settlement at the interfaces of the organic solvents and water. However, zoospores settled and created mycelial networks only at HD-water interfaces. Both bacteria diminished the toxic influence of PAHs on zoospore formation and taxis, and they did not interrupt zoospore settlement. The results suggest that zoospore development could be applicable for toxicity assessment of PAHs and enhancement of their bioavailability. Microbial interactions during both swimming modes and community formation at pollutant interfaces were revealed as major factors that have potential relevance to bioremediation.
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Affiliation(s)
- Rungroch Sungthong
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, 41080 Seville, Spain
| | - Pieter van West
- Aberdeen Oomycete Laboratory, University of Aberdeen, Institute of Medical Sciences, Foresterhill, AB25 2ZD Aberdeen UK
| | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, 41080 Seville, Spain
| | - Jose Julio Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, 41080 Seville, Spain.
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Ren G, Ren W, Teng Y, Li Z. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil. Front Microbiol 2015; 6:22. [PMID: 25688237 PMCID: PMC4311681 DOI: 10.3389/fmicb.2015.00022] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/08/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the potential for Polycyclic aromatic hydrocarbons (PAH) degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene) at three dosages (5, 30, and 70 mg ⋅ kg(-1)). Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA) quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1) at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0%) including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while three phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria) were significantly increased; and (2) at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community level.
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Affiliation(s)
- Gaidi Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
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Phytomediated biostimulation of the autochthonous bacterial community for the acceleration of the depletion of polycyclic aromatic hydrocarbons in contaminated sediments. BIOMED RESEARCH INTERNATIONAL 2014; 2014:891630. [PMID: 25170516 PMCID: PMC4142154 DOI: 10.1155/2014/891630] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 11/17/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a large group of organic contaminants causing hazards to organisms including humans. The objective of the study was to validate the vegetation of dredged sediments with Phragmites australis as an exploitable biostimulation approach to accelerate the depletion of PAHs in nitrogen spiked sediments. Vegetation with Phragmites australis resulted in being an efficient biostimulation approach for the depletion of an aged PAHs contamination (229.67 ± 15.56 μg PAHs/g dry weight of sediment) in dredged sediments. Phragmites australis accelerated the oxidation of the PAHs by rhizodegradation. The phytobased approach resulted in 58.47% of PAHs depletion. The effects of the treatment have been analyzed in terms of both contaminant depletion and changes in relative abundance of the metabolically active Gram positive and Gram negative PAHs degraders. The metabolically active degraders were quantified both in the sediments and in the root endospheric microbial community. Quantitative real-time PCR reactions have been performed on the retrotranscribed transcripts encoding the Gram positive and Gram negative large α subunit (RHDα) of the aromatic ring hydroxylating dioxygenases. The Gram positive degraders resulted in being selectively favored by vegetation with Phragmites australis and mandatory for the depletion of the six ring condensed indeno[1,2,3-cd]pyrene and benzo[g,h,i]perylene.
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30
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Genetic and metabolic analysis of the carbofuran catabolic pathway in Novosphingobium sp. KN65.2. Appl Microbiol Biotechnol 2014; 98:8235-52. [DOI: 10.1007/s00253-014-5858-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 12/12/2022]
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31
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Jiao L, Chen H, Meng W, Lei K, Zheng B. PAHs biodegradation in intertidal surface sediment by indigenous microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:6463-6471. [PMID: 24504772 DOI: 10.1007/s11356-013-2480-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/17/2013] [Indexed: 06/03/2023]
Abstract
In this study, the 30-day aerobic microorganism-mediated biodegradation of polycyclic aromatic hydrocarbons (PAHs) was investigated in four size fractions (i.e., <0.002, 0.002-0.031, 0.031-0.063 and >0.063 mm) of sand-dominated sediment S1 and mud-dominated S2 collected from intertidal zones in Bohai Bay (China). Prior to biodegradation, the total quantity of phenanthrene, fluoranthene and pyrene comprised more than 80% of the total quantity of 16 EPA-priority PAHs in each size fraction, with the exception of 70.33% found in the >0.063 mm fraction of sediment S1. Among the three dominant compounds, the intermediate size fraction (0.031-0.063 mm) showed higher levels of biodegradation than other size fractions in sediment S1 and S2. After pooling data from sediment S1 and S2 for joint analysis, it was observed that the biodegraded portion of the three dominant compounds showed negative correlations with both total organic carbon (TOC) and humic coverage index (HCI) in the size fractions. The observed negative correlation with TOC was in agreement with findings in many other studies, but the negative correlation with HCI had not been observed in early studies, which only investigated aged sediment/soil samples. The findings in this study indicated that the greatest bioavailability of PAHs in intertidal surface sediment may be present in sediment particles of intermediate size and mobility, and that intertidal sediment particles are less likely to experience sufficient ageing given periodical tidal disturbance. These findings have important implications for the assessment of the environmental fate of PAHs in intertidal regions.
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Affiliation(s)
- Lixin Jiao
- Institute of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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32
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Han XM, Liu YR, Zheng YM, Zhang XX, He JZ. Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:9754-9763. [PMID: 24777329 DOI: 10.1007/s11356-014-2928-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.
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Affiliation(s)
- Xue-Mei Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Elango V, Urbano M, Lemelle KR, Pardue JH. Biodegradation of MC252 oil in oil:sand aggregates in a coastal headland beach environment. Front Microbiol 2014; 5:161. [PMID: 24782849 PMCID: PMC3989593 DOI: 10.3389/fmicb.2014.00161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Unique oil:sand aggregates, termed surface residue balls (SRBs), were formed on coastal headland beaches along the northern Gulf of Mexico as emulsified MC252 crude oil mixed with sand following the Deepwater Horizon spill event. The objective of this study is to assess the biodegradation potential of crude oil components in these aggregates using multiple lines of evidence on a heavily-impacted coastal headland beach in Louisiana, USA. SRBs were sampled over a 19-month period on the supratidal beach environment with reasonable control over and knowledge of the residence time of the aggregates on the beach surface. Polycyclic aromatic hydrocarbons (PAHs) and alkane concentration ratios were measured including PAH/C30-hopane, C2/C3 phenanthrenes, C2/C3 dibenzothiophenes and alkane/C30-hopane and demonstrated that biodegradation was occurring in SRBs in the supratidal. These biodegradation reactions occurred over time frames relevant to the coastal processes moving SRBs off the beach. In contrast, submerged oil mat samples from the intertidal did not demonstrate chemical changes consistent with biodegradation. Review and analysis of additional biogeochemical parameters suggested the existence of a moisture and nutrient-limited biodegradation regime on the supratidal beach environment. At this location, SRBs possess moisture contents <2% and molar C:N ratios from 131–323, well outside of optimal values for biodegradation in the literature. Despite these limitations, biodegradation of PAHs and alkanes proceeded at relevant rates (2–8 year−1) due in part to the presence of degrading populations, i.e., Mycobacterium sp., adapted to these conditions. For submerged oil mat samples in the intertidal, an oxygen and salinity-impacted regime is proposed that severely limits biodegradation of alkanes and PAHs in this environment. These results support the hypothesis that SRBs deposited at different locations on the beach have different biogeochemical characteristics (e.g., moisture, salinity, terminal electron acceptors, nutrient, and oil composition) due, in part, to their location on the landscape.
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Affiliation(s)
- Vijaikrishnah Elango
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - Marilany Urbano
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - Kendall R Lemelle
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - John H Pardue
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
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Li J, Ye Q, Gan J. Degradation and transformation products of acetaminophen in soil. WATER RESEARCH 2014; 49:44-52. [PMID: 24316789 DOI: 10.1016/j.watres.2013.11.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 11/05/2013] [Accepted: 11/09/2013] [Indexed: 05/17/2023]
Abstract
Acetaminophen is the most widely used human medicine. Trace levels of acetaminophen are frequently detected in treated wastewater and the impacted surface or groundwater resources. However, even though soil is a primary receiving compartment, the fate of acetaminophen in soil is poorly known, including in particular the potential for the formation of incomplete degradation products that may have altered biological activity and mobility. In this study, using both (14)C-labeling and LC-MS/MS techniques, we evaluated the dissipation routes and transformation pathways of acetaminophen in soils under a range of conditions. Throughout 120-d aerobic incubation, up to 17.0 ± 0.8% of (14)C-acetaminophen was mineralized, but mineralization was greatly inhibited after sterilization or amendment of biosolids. Immediately after treatment, the majority of (14)C-residue became non-extractable or bound, with the level accounting for 73.4-93.3% of the applied amount at the end of incubation. A total of 8 intermediates were identified, including 3-hydroxyacetaminophen, hydroquinone, 1, 4-benzoquinone, N-acetyl-p-benzoquinone imine, p-acetanisidide, 4-methoxyphenol, 2-hexenoic acid, and 1, 4-dimethoxybenzene. Mineralization and rapid conversion to bound residues suggest that acetaminophen is quickly detoxified in soil, decreasing the potential for off-site transport such as leaching or runoff. On the other hand, the formation of a large number of degradation intermediates, and their potential biological activity, may pose unknown risks, such as accumulation into edible plants. This risk warrants further investigation.
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Affiliation(s)
- Juying Li
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA; Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Qingfu Ye
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Jay Gan
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
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Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants. ISME JOURNAL 2014; 8:1289-300. [PMID: 24430482 DOI: 10.1038/ismej.2013.233] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/15/2013] [Accepted: 11/26/2013] [Indexed: 11/09/2022]
Abstract
Many organic pollutants are readily degradable by microorganisms in soil, but the importance of soil organic matter for their transformation by specific microbial taxa is unknown. In this study, sorption and microbial degradation of phenol and 2,4-dichlorophenol (DCP) were characterized in three soil variants, generated by different long-term fertilization regimes. Compared with a non-fertilized control (NIL), a mineral-fertilized NPK variant showed 19% and a farmyard manure treated FYM variant 46% more soil organic carbon (SOC). Phenol sorption declined with overall increasing SOC because of altered affinities to the clay fraction (soil particles <2 mm in diameter). In contrast, DCP sorption correlated positively with particulate soil organic matter (present in the soil particle fractions of 63-2000 μm). Stable isotope probing identified Rhodococcus, Arthrobacter (both Actinobacteria) and Cryptococcus (Basidiomycota) as the main degraders of phenol. Rhodococcus and Cryptococcus were not affected by SOC, but the participation of Arthrobacter declined in NPK and even more in FYM. (14)C-DCP was hardly metabolized in the NIL variant, more efficiently in FYM and most in NPK. In NPK, Burkholderia was the main degrader and in FYM Variovorax. This study demonstrates a strong effect of SOC on the partitioning of organic pollutants to soil particle size fractions and indicates the profound consequences that this process could have for the diversity of bacteria involved in their degradation.
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Johnsen AR, Styrishave B, Aamand J. Quantification of small-scale variation in the size and composition of phenanthrene-degrader populations and PAH contaminants in traffic-impacted topsoil. FEMS Microbiol Ecol 2014; 88:84-93. [DOI: 10.1111/1574-6941.12272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/02/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Anders R. Johnsen
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K Denmark
| | - Bjarne Styrishave
- Toxicology Laboratory; Department of Pharmacy; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen K Denmark
| | - Jens Aamand
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K Denmark
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Urbano M, Elango V, Pardue JH. Biogeochemical characterization of MC252 oil:sand aggregates on a coastal headland beach. MARINE POLLUTION BULLETIN 2013; 77:183-191. [PMID: 24210008 DOI: 10.1016/j.marpolbul.2013.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 06/02/2023]
Abstract
MC252 oil:sand aggregates, termed surface residue balls (SRBs), were sampled for physical, chemical and microbial characteristics from different tidal zones on a coastal headland beach in Louisiana, USA. Supratidal SRBs were smaller, had low moisture content, and salinities that were <2 ppt. Intertidal SRBs were hypersaline and had higher N and sulfate concentrations, consistent with regular tidal inundation. Crude oil components were highest in the intertidal "oil mat" SRBs with C1- and C2-phenanthrenes, C2- and C3-dibenzothiophenes comprising the majority of the PAH concentrations. In the other SRB categories, PAHs and alkanes were depleted and profiles were skewed toward higher molecular weight compounds. Oxygen microelectrode measurements demonstrated that saturated O2 is present immediately after wetting, but O2 consumption in the interior of the aggregate occurs after a few days. Microbial populations varied with position on the beach but sequences similar to known PAH-degrading taxa (Mycobacterium sp. and Stenotrophomonas sp.) were observed.
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Affiliation(s)
- Marilany Urbano
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States
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Radomski N, Roguet A, Lucas FS, Veyrier FJ, Cambau E, Accrombessi H, Moilleron R, Behr MA, Moulin L. atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples. BMC Microbiol 2013; 13:277. [PMID: 24299240 PMCID: PMC4219376 DOI: 10.1186/1471-2180-13-277] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background The environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets. Results Among the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples. Conclusions The results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.
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Affiliation(s)
- Nicolas Radomski
- Laboratoire Eau Environnement Systèmes Urbains (Leesu) UMR MA 102-AgroParisTech, Université Paris-Est, 6-8 avenue Blaise Pascal Cité, Descartes, FR 77455, Champs sur Marne, France.
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Ortega-Calvo JJ, Tejeda-Agredano MC, Jimenez-Sanchez C, Congiu E, Sungthong R, Niqui-Arroyo JL, Cantos M. Is it possible to increase bioavailability but not environmental risk of PAHs in bioremediation? JOURNAL OF HAZARDOUS MATERIALS 2013; 261:733-45. [PMID: 23583067 DOI: 10.1016/j.jhazmat.2013.03.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 02/28/2013] [Accepted: 03/16/2013] [Indexed: 05/21/2023]
Abstract
The current poor predictability of end points associated with the bioremediation of polycyclic aromatic hydrocarbons (PAHs) is a large limitation when evaluating its viability for treating contaminated soils and sediments. However, we have seen a wide range of innovations in recent years, such as an the improved use of surfactants, the chemotactic mobilization of bacterial inoculants, the selective biostimulation at pollutant interfaces, rhizoremediation and electrobioremediation, which increase the bioavailability of PAHs but do not necessarily increase the risk to the environment. The integration of these strategies into practical remediation protocols would be beneficial to the bioremediation industry, as well as improve the quality of the environment.
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Affiliation(s)
- J J Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apartado 1052, E-41080 Seville, Spain.
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Li X, Li X, Wang J, Wang X, Sun J, Su Z, Zhang H, Li P. Profiles ofMycobacteriumcommunities under polycyclic aromatic hydrocarbon contamination stress in the Shenfu Irrigation Area, northeast China. Can J Microbiol 2013; 59:694-700. [DOI: 10.1139/cjm-2013-0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Indigenous Mycobacterium communities play an important role in the degradation of polycyclic aromatic hydrocarbons (PAHs), but little is known about Mycobacterium distribution in situ at PAH-contaminated sites. In this study, the diversity and distribution of Mycobacterium communities were investigated in sediments and soils at sites upstream, midstream, and downstream of an oil-sewage irrigation channel, using denaturing gradient gel electrophoresis (DGGE). The results show that heavy PAH contamination in upstream sites negatively affected Mycobacterium community diversity compared with midstream and downstream sites in all 3 sample types (sediments, corn field soils, and rice field soils). There was a correlation between the distribution of Mycobacterium communities and PAH contamination, as indicated by canonical correspondence analysis. Mycobacterium diversity and distribution was found to vary between the 3 sample types.
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Affiliation(s)
- Xinyu Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Xu Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Jian Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Xiujuan Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Jian Sun
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Zhencheng Su
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Huiwen Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
| | - Peijun Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, People’s Republic of China
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Pernot A, Ouvrard S, Leglize P, Faure P. Protective role of fine silts for PAH in a former industrial soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 179:81-87. [PMID: 23665618 DOI: 10.1016/j.envpol.2013.03.068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 06/02/2023]
Abstract
An original combined organic geochemistry and soil science approach was used to elucidate PAH availability controlling factors in a multi-contaminated industrial soil. Water granulodensimetric fractionation was applied to obtain five water-stable material fractions. These were characterized by elemental, molecular and mineral analysis, and microscopic observations. Among the different fractions, fine silts distinguished themselves by higher carbon and nitrogen contents, lower C/N ratio, an enrichment in total PAH and especially high molecular weight compounds, a coal tar signature and the lowest PAH availability. This fine silt fraction seemed to play a protective role for PAH that might be explained by its size and/or its specific reactivity. The mineral phases present in this fraction were proposed to explain the protection of organic matter. This led to a specific molecular signature of OM, having higher sorption properties both processes (sorption and mineral-bound protection) resulting in a lower PAH availability.
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Affiliation(s)
- Audrey Pernot
- Laboratoire Sols et Environnement, UMR1120, Université de Lorraine, Vandœuvre-lès-Nancy F-54518, France
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Dunon V, Sniegowski K, Bers K, Lavigne R, Smalla K, Springael D. High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments. FEMS Microbiol Ecol 2013; 86:415-31. [PMID: 23802695 DOI: 10.1111/1574-6941.12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 04/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022] Open
Abstract
Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071-specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.
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Affiliation(s)
- Vincent Dunon
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity. PLoS One 2013; 8:e68648. [PMID: 23874704 PMCID: PMC3715504 DOI: 10.1371/journal.pone.0068648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/30/2013] [Indexed: 12/30/2022] Open
Abstract
Background Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected.
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Bers K, De Mot R, Springael D. In situresponse of the linuron degradation potential to linuron application in an agricultural field. FEMS Microbiol Ecol 2013; 85:403-16. [DOI: 10.1111/1574-6941.12129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 03/25/2013] [Accepted: 04/01/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Karolien Bers
- Division of Soil and Water Management; KU Leuven; Leuven Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics; KU Leuven; Leuven Belgium
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Leuven Belgium
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Li J, Dodgen L, Ye Q, Gan J. Degradation kinetics and metabolites of carbamazepine in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:3678-84. [PMID: 23506704 DOI: 10.1021/es304944c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The antiepileptic drug carbamazepine (CBZ) is one of the most frequently detected human pharmaceuticals in wastewater effluents and biosolids. Soil is a primary environmental compartment receiving CBZ through wastewater irrigation and biosolid application. In this study, we explored the transformation of CBZ to biologically active intermediates in soil. Both (14)C labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to track transformation kinetics and identify major degradation intermediates. Through 120 days of incubation under aerobic conditions, mineralization of CBZ did not exceed 2% of the spiked rate in different soils. Amendment of biosolids further suppressed mineralization. The fraction of non-extractable (i.e., bound) residue also remained negligible (<5%). On the other hand, CBZ was transformed to a range of degradation intermediates, including 10,11-dihydro-10-hydroxycarbamazepine, carbamazepine-10,11-epoxide, acridone-N-carbaldehyde, 4-aldehyde-9-acridone, and acridine, of which acridone-N-carbaldehyde was formed in a large fraction and appeared to be recalcitrant to further degradation. Electrocyclization, ring cleavage, hydrogen shift, carbonylation, and decarbonylation contributed to CBZ transformative reactions in soil, producing biologically active products. The persistence of the parent compound and formation of incomplete intermediates suggest that CBZ has a high risk for off-site transport from soil, such as accumulation into plants and contamination of groundwater.
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Affiliation(s)
- Juying Li
- Department of Environmental Sciences, University of California-Riverside, Riverside, California 92521, United States
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Babin D, Ding GC, Pronk GJ, Heister K, Kögel-Knabner I, Smalla K. Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene. FEMS Microbiol Ecol 2013; 86:3-14. [DOI: 10.1111/1574-6941.12058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/06/2012] [Accepted: 12/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | | | - Katja Heister
- Lehrstuhl für Bodenkunde; Technische Universität München; Freising-Weihenstephan; Germany
| | | | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
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Van Dierdonck J, Van den Broeck R, Vervoort E, D’haeninck P, Springael D, Van Impe J, Smets I. Does a change in reactor loading rate affect activated sludge bioflocculation? Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Haest PJ, Springael D, Seuntjens P, Smolders E. Self-inhibition can limit biologically enhanced TCE dissolution from a TCE DNAPL. CHEMOSPHERE 2012; 89:1369-1375. [PMID: 22749126 DOI: 10.1016/j.chemosphere.2012.05.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/28/2012] [Accepted: 05/30/2012] [Indexed: 06/01/2023]
Abstract
Biodegradation of trichloroethene (TCE) near a Dense Non Aqueous Phase Liquid (DNAPL) can enhance the dissolution rate of the DNAPL by increasing the concentration gradient at the DNAPL-water interface. Two-dimensional flow-through sand boxes containing a TCE DNAPL and inoculated with a TCE dechlorinating consortium were set up to measure this bio-enhanced dissolution under anaerobic conditions. The total mass of TCE and daughter products in the effluent of the biotic boxes was 3-6 fold larger than in the effluent of the abiotic box. However, the mass of daughter products only accounted for 19-55% of the total mass of chlorinated compounds in the effluent, suggesting that bio-enhanced dissolution factors were maximally 1.3-2.2. The enhanced dissolution most likely primarily resulted from variable DNAPL distribution rather than biodegradation. Specific dechlorination rates previously determined in a stirred liquid medium were used in a reactive transport model to identify the rate limiting factors. The model adequately simulated the overall TCE degradation when predicted resident microbial numbers approached observed values and indicated an enhancement factor for TCE dissolution of 1.01. The model shows that dechlorination of TCE in the 2D box was limited due to the short residence time and the self-inhibition of the TCE degradation. A parameter sensitivity analysis predicts that the bio-enhanced dissolution factor for this TCE source zone can only exceed a value of 2 if the TCE self-inhibition is drastically reduced (when a TCE tolerant dehalogenating community is present) or if the DNAPL is located in a low-permeable layer with a small Darcy velocity.
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Affiliation(s)
- P J Haest
- Division Soil and Water Management, Catholic University of Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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Lu Z, Zeng F, Xue N, Li F. Occurrence and distribution of polycyclic aromatic hydrocarbons in organo-mineral particles of alluvial sandy soil profiles at a petroleum-contaminated site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 433:50-57. [PMID: 22766427 DOI: 10.1016/j.scitotenv.2012.06.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 05/26/2012] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
The occurrence and the distribution of 16 USEPA priority pollutants polycyclic aromatic hydrocarbons (PAHs) were investigated in two alluvial sandy soil profiles and in their four sizes of organo-mineral particles (<2 μm clay, 2-20 μm silt, 20-200 μm fine sand, and >200 μm coarse sand) beside a typical oil sludge storage site in eastern China. PAHs were mainly enriched in the surface soil (0-20 cm) and the concentrations declined in deeper soils, from 3.68 to 0.128 μg/g in profile 1 and 10.8 to 0.143 μg/g in profile 2 (dry wt.). The PAHs in the upper soil layers of this study site mainly came from combustion pollution, whereas in the lower soil layers petroleum contamination became the major source of PAHs. The content of different sized organo-mineral particles of this alluvial sandy soil decreased in the following order: fine sand>coarse sand>silt>clay. X-ray diffraction (XRD) results showed that all the different sized soil fractions of this study site were dominated by quartz, calcite and feldspar. The particle surface became smoother with size increasing as shown by scanning electron microscope (SEM) images. PAH concentrations varied largely in different sized soil fractions. The highest PAH concentration was associated with clay and decreased in the order: clay>silt>coarse sand>fine sand. Soil organic matter (SOM) content, mineral composition and particle surface characteristics were suggested as three main factors affecting the distribution of PAHs in different sized organo-mineral particles. This study will help to understand the distribution and transport characteristics of PAHs in soil profiles at petroleum-contaminated sites.
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Affiliation(s)
- Zhe Lu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Anwai, Dayangfang 8, Beijing 100012, PR China
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Ding GC, Heuer H, Smalla K. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Front Microbiol 2012; 3:290. [PMID: 22934091 PMCID: PMC3423926 DOI: 10.3389/fmicb.2012.00290] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/23/2012] [Indexed: 11/13/2022] Open
Abstract
Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.
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Affiliation(s)
- Guo-Chun Ding
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants Braunschweig, Germany
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