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Yang B, Zhou M, Meng Y, Chen K, Xu J, Huang X, Liu Y, Li L, Ma L, Chen M. Hydrocarbons removal and microbial community succession in petroleum-contaminated soil under hydrogen peroxide treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:27081-27091. [PMID: 36374389 DOI: 10.1007/s11356-022-23875-z] [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: 05/03/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Chemical oxidation as a pretreatment step coupled with bioremediation for petroleum-contaminated soil may pose serious impacts on indigenous microorganisms and the available nutrients. Petroleum-contaminated soil were treated by hydrogen peroxide (H2O2) at initial concentrations of 105 mM (HH), 21 mM (HL), and 105 mM in three equal amounts (HT) without adding any external catalyst. The contents of total petroleum hydrocarbons (TPH) and dissolved nutrients (total organic compounds, nitrogen, and phosphate), and the indigenous bacteria community succession (analyzed by high-throughput sequencing of 16S rDNA) were investigated over 50 days. Compared to the control treatment without H2O2 addition, H2O2 treatments for the petroleum-contaminated soil significantly promoted the TPH removal especially in the first 4 days and impacted the contents of dissolved nutrients. Both of chemical oxidation and nutrients contributed to microbial community structure changes in alpha diversity. Although the soil microbial community structure had undergone significant changes after different chemical oxidation pretreatments, Firmicutes, Proteobacteria, Gemmatimonadetes, and Actinobacteria were the main bacterial phyla. Compared with adding H2O2 at one time, H2O2 added in stepwise was beneficial to indigenous bacterial diversity recovery and TPH removal. H2O2 oxidation treatments showed a great influence on the microbial community structures in the start-up stage, while recovery time rather than the oxidation treatments presented greater effects on the composition of the microbial community structure with the incubation time extended. Therefore, adding H2O2 as pretreatment for petroleum-contaminated soil showed little effect on the structure of soil indigenous microbial community from a long-term scale, and was conducive to the continuous removal of TPH by indigenous microorganisms.
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Affiliation(s)
- Bing Yang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China.
- Institute of Industrial Hazardous Waste Disposal and Utilization, Southwest Petroleum University, Chengdu, 610500, Sichuan, China.
- Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Chengdu, 610500, Sichuan, China.
| | - Mi Zhou
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Yuan Meng
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Keming Chen
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Jie Xu
- Safety, Environment and Technology Supervision Research Institute of PetroChina Southwest Oil and Gas Field Company, Chengdu, 610056, Sichuan, China
| | - Xiangfu Huang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Yucheng Liu
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
- Institute of Industrial Hazardous Waste Disposal and Utilization, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Lingli Li
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Lili Ma
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Mingyan Chen
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
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Yang C, Huang Y, Long B, Gao X. Effects of biodegradable and polyethylene film mulches and their residues on soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:89698-89711. [PMID: 35854074 DOI: 10.1007/s11356-022-22014-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
To investigate the effects of plastic film mulches and their residual films after use on soil bacterial communities, mulching experiment and the subsequent residual film experiment were conducted on winter-planting potato field in two locations. During mulching experiment, treatments biodegradable film mulch (BM) and PE film mulch (PM) reduced soil nutrient regarding available nitrogen and available potassium, as well as microbial biomass carbon (MBC), but increased urease activity, as compared to treatment no film mulch (NM). Soil moisture was significantly elevated by mulching practices and correlated with more microbial phyla than the other tested soil properties, indicating its important role in shaping soil bacterial communities. In addition, mulching practices increased alpha diversity of soil bacteria, although location heterogeneity was observed. Network analyses showed that both treatments BM and PM promoted the interrelations within bacterial communities and harbored more keystone taxa than treatment NM. During residual film experiment, residual films from BM and PM were incorporated into soil after harvest of potato. Treatment residual biodegradable film (RBF) significantly increased the content of MBC and activity of β-glucosidase (BG) as compared to treatments residual PE film (RPF) and no residual film (NRF), and BG had the most correlations with microbial phyla among all the tested soil properties. Treatments RBF and RPF increased the relative abundance of some dominant bacterial phyla, including Bacteroidetes, Actinobacteria, and Chlorofexi, and enhanced the interrelations within bacterial community, whereas more keystone taxa were harbored by treatment RBF, due to the increase of keystone taxa in phyla Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. These results indicate that the indirect effects of biodegradable and PE film mulch as a soil surface barrier on soil are similar, whereas their direct effects via incorporation into soil as residual films show specificity.
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Affiliation(s)
- Chong Yang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China.
- Guangdong Biomaterials Engineering Technology Research Center, Guangzhou, 510316, China.
| | - Yaozhu Huang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
- Guangdong Biomaterials Engineering Technology Research Center, Guangzhou, 510316, China
| | - Bibo Long
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
- Guangdong Biomaterials Engineering Technology Research Center, Guangzhou, 510316, China
| | - Xuhua Gao
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
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Chai G, Wang D, Shan J, Jiang C, Yang Z, Liu E, Meng H, Wang H, Wang Z, Qin L, Xi J, Ma Y, Li H, Qian Y, Li J, Lin Y. Accumulation of high-molecular-weight polycyclic aromatic hydrocarbon impacted the performance and microbial ecology of bioretention systems. CHEMOSPHERE 2022; 298:134314. [PMID: 35292274 DOI: 10.1016/j.chemosphere.2022.134314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Bioretention has been considered as an effective management practice for urban stormwater in the removal of pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the accumulation of high-molecular-weight (HMW) PAHs in bioretention systems and their potential impact on the pollutants removal performance and microbial ecology are still not fully understood. In this study, comparisons of treatment effectiveness, enzyme activity and microbial community in bioretention systems with different types of media amendments were carried out at different spiking levels of pyrene (PYR). The results showed that the removal efficiencies of chemical oxygen demand (COD) and total nitrogen in the bioretention systems were negatively impacted by the PYR levels. The relative activities of soil dehydrogenase and urease were increasingly inhibited by the elevated PYR level, indicating the declining microbial activity regarding organic matter decomposition. The spiking of PYR negatively affected microbial diversity, and distinct time- and influent-dependent changes in microbial communities were observed. The relative abundance of PAH-degrading microorganisms increased in PYR-spiked systems, while the abundance of nitrifiers decreased. The addition of media amendments was beneficial for the enrichment of microorganisms that are more resistant to PYR-related stress, therefore elevating the COD concentration removal rate by ∼50%. This study gives new insight into the multifaceted impacts of HMW PAH accumulation on microbial fingerprinting and enzyme activities, which may provide guidance on better stormwater management practices via bioretention in terms of improved system longevity and performance.
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Affiliation(s)
- Guodong Chai
- Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Dongqi Wang
- Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Jiaqi Shan
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Chunbo Jiang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Zhangjie Yang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Enyu Liu
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Haiyu Meng
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Hui Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Zhe Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Lu Qin
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Jiayao Xi
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Yuenan Ma
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Huaien Li
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Yishi Qian
- Xi'an Modern Chemistry Research Institute, Xi'an, Shaanxi 710065, China
| | - Jiake Li
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China.
| | - Yishan Lin
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China.
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Vanhoutte I, De Tender C, Demeyere K, Abdallah MF, Ommeslag S, Vermeir P, Saeger SD, Debode J, Meyer E, Croubels S, Audenaert K, De Gelder L. Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells. Toxins (Basel) 2021; 13:toxins13080552. [PMID: 34437423 PMCID: PMC8402469 DOI: 10.3390/toxins13080552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH2O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.
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Affiliation(s)
- Ilse Vanhoutte
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
- Computer Science and Statistics, Department of Applied Mathematics, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kristel Demeyere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Mohamed F. Abdallah
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA), Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Evelyne Meyer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Leen De Gelder
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
- Correspondence: ; Tel.: +32-9-243-24-75
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Shi Y, Xiao Y, Li Z, Zhang X, Liu T, Li Y, Pan Y, Yan W. Microorganism structure variation in urban soil microenvironment upon ZnO nanoparticles contamination. CHEMOSPHERE 2021; 273:128565. [PMID: 33087259 DOI: 10.1016/j.chemosphere.2020.128565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Nanoparticles (NPs) sink into the soil via agricultural spreading, surface water, atmospheric deposition, and industrial emission, which affects plant growth and soil microenvironment. To understand how NPs influence urban soil microenvironment, the effect of typical nano-pollutants zinc oxide nanoparticles (ZnONPs) was investigated in urban solid-waste land. Pokeweed (Phytolacca Americana L.) soil samples from solid-waste land were collected and exposed to 200, 500, and 1000 mg kg-1 ZnONPs. The physiological characteristics of pokeweed, soil bacterial community composition, and soil physiochemical properties and enzymatic activities were determined. Our results show that pokeweed growth was slightly inhibited, and soil acid-base homeostasis was affected in ZnONPs-contaminated samples. Meanwhile, enzymatic activities related to soil C cycle were enhanced, and bacterial community structure at the phylum and genus levels was altered. Specifically, the abundance of hydrocarbon-degrading taxa reduced substantially upon ZnONPs exposure. The phenoloxidase (PPO) activity and the refractory hydrocarbon-degrading bacteria Bacteroidetes was adversely affected by ZnONPs exposure. In addition, Subgroup_10 of Acidobacteria was identified as an indicator of soil ZnONPs contamination. Our study detected changes in plant growth, soil environmental factors, and soil microbe community composition in urban solid-waste land treated by ZnONPs. The results of this research provide evidence for ZnONPs toxicology on urban soil microenvironment.
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Affiliation(s)
- Yang Shi
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Yunmu Xiao
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Ziqian Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Xuyuan Zhang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Ting Liu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Yong Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China.
| | - Yuliang Pan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Wende Yan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China.
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Medaura MC, Guivernau M, Moreno-Ventas X, Prenafeta-Boldú FX, Viñas M. Bioaugmentation of Native Fungi, an Efficient Strategy for the Bioremediation of an Aged Industrially Polluted Soil With Heavy Hydrocarbons. Front Microbiol 2021; 12:626436. [PMID: 33868189 PMCID: PMC8044458 DOI: 10.3389/fmicb.2021.626436] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/10/2021] [Indexed: 01/30/2023] Open
Abstract
The concurrence of structurally complex petroleum-associated contaminants at relatively high concentrations, with diverse climatic conditions and textural soil characteristics, hinders conventional bioremediation processes. Recalcitrant compounds such as high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and heavy alkanes commonly remain after standard soil bioremediation at concentrations above regulatory limits. The present study assessed the potential of native fungal bioaugmentation as a strategy to promote the bioremediation of an aged industrially polluted soil enriched with heavy hydrocarbon fractions. Microcosms assays were performed by means of biostimulation and bioaugmentation, by inoculating a defined consortium of six potentially hydrocarbonoclastic fungi belonging to the genera Penicillium, Ulocladium, Aspergillus, and Fusarium, which were isolated previously from the polluted soil. The biodegradation performance of fungal bioaugmentation was compared with soil biostimulation (water and nutrient addition) and with untreated soil as a control. Fungal bioaugmentation resulted in a higher biodegradation of total petroleum hydrocarbons (TPH) and of HMW-PAHs than with biostimulation. TPH (C14-C35) decreased by a 39.90 ± 1.99% in bioaugmented microcosms vs. a 24.17 ± 1.31% in biostimulated microcosms. As for the effect of fungal bioaugmentation on HMW-PAHs, the 5-ringed benzo(a)fluoranthene and benzo(a)pyrene were reduced by a 36% and 46%, respectively, while the 6-ringed benzoperylene decreased by a 28%, after 120 days of treatment. Biostimulated microcosm exhibited a significantly lower reduction of 5- and 6-ringed PAHs (8% and 5% respectively). Higher TPH and HMW-PAHs biodegradation levels in bioaugmented microcosms were also associated to a significant decrease in acute ecotoxicity (EC50) by Vibrio fischeri bioluminiscence inhibition assays. Molecular profiling and counting of viable hydrocarbon-degrading bacteria from soil microcosms revealed that fungal bioaugmentation promoted the growth of autochthonous active hydrocarbon-degrading bacteria. The implementation of such an approach to enhance hydrocarbon biodegradation should be considered as a novel bioremediation strategy for the treatment of the most recalcitrant and highly genotoxic hydrocarbons in aged industrially polluted soils.
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Affiliation(s)
| | - Miriam Guivernau
- GIRO Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain
| | - X. Moreno-Ventas
- Department of Sciences and Techniques in Water and Environment, University of Cantabria, Santander, Spain
| | | | - Marc Viñas
- GIRO Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain
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Zhang M, Zhao Y, Qin X, Jia W, Chai L, Huang M, Huang Y. Microplastics from mulching film is a distinct habitat for bacteria in farmland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:470-478. [PMID: 31254812 DOI: 10.1016/j.scitotenv.2019.06.108] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 05/07/2023]
Abstract
Microplastics, as an emerging pollutant of global importance, have been well documented in aquatic ecosystems. However, little is known about the effects of microplastics on agroecosystems, particularly for soil microbial communities. Herein, microplastics collected from cotton fields in Xinjiang, China, were analysed with a scanning electron microscope (SEM) and high-throughput sequencing to investigate the attached bacterial communities. Microplastic surfaces, especially pits and flakes, were colonized by various microorganisms, suggesting active hydrolysis of plastic debris. The bacterial communities colonizing microplastics were significantly different in structure from those in the surrounding soil, plant litter and macroplastics. In addition, statistical analysis of differentially abundant OTUs showed that microplastics serve as a "special microbial accumulator" in farmland soil, enriching some taxa that degrade polyethylene, such as Actinobacteria, Bacteroidetes and Proteobacteria. Co-occurrence network analysis revealed that the biotic interactions between microorganisms on microplastics are as complex as those in soil, and Acidobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes are considered keystone species in bacterial communities. Collectively, the findings imply that microplastics acted as a distinct habitat for bacteria in farmland soil, which increases our understanding of microplastic pollution.
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Affiliation(s)
- Mengjun Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yanran Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Xiao Qin
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China.
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8
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Jiao S, Luo Y, Lu M, Xiao X, Lin Y, Chen W, Wei G. Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 225:497-505. [PMID: 28336094 DOI: 10.1016/j.envpol.2017.03.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/16/2017] [Accepted: 03/07/2017] [Indexed: 05/20/2023]
Abstract
Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for β-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yantao Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Mingmei Lu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiao Xiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Parulekar NN, Kolekar P, Jenkins A, Kleiven S, Utkilen H, Johansen A, Sawant S, Kulkarni-Kale U, Kale M, Sæbø M. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PLoS One 2017; 12:e0173408. [PMID: 28282404 PMCID: PMC5345797 DOI: 10.1371/journal.pone.0173408] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/19/2017] [Indexed: 11/19/2022] Open
Abstract
Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.
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MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Cyanobacteria/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Enzyme-Linked Immunosorbent Assay
- High-Throughput Nucleotide Sequencing
- Lakes/microbiology
- Microcystins/analysis
- Microcystis/genetics
- Microcystis/metabolism
- Norway
- Phytoplankton/genetics
- Phytoplankton/growth & development
- Proteobacteria/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Niranjan Nitin Parulekar
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
- * E-mail:
| | - Pandurang Kolekar
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Andrew Jenkins
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Synne Kleiven
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Hans Utkilen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Anette Johansen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Sangeeta Sawant
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mohan Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mona Sæbø
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
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Mehri I, Lajnef R, Rejab AB, Khessairi A, Cherif H, Ouzari H, Hassen A. Biofilms in bioremediation and wastewater treatment: characterization of bacterial community structure and diversity during seasons in municipal wastewater treatment process. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:3519-3530. [PMID: 27878485 DOI: 10.1007/s11356-016-8090-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/09/2016] [Indexed: 05/02/2023]
Abstract
The bacterial community structure and diversity were assessed at the scale of rotating biodisk procedure (RB) in a semi-industrial pilot plant. As well, the Salmonella community was particularly monitored, and the effects of ultraviolet (UV-C254) on the bacterial community were studied. The identification of dominant bacteria revealed the presence of beneficial and useful species that could play an important role in the process of wastewater purification. Several species as Enterobacter agglomerans, Cronobacter sakazakii, and Pantoea agglomerans known for their bioremediation activities were revealed in the majority of biofilm samples. Common detection of Salmonella community provides evidence that the RB system did not seriously affect Salmonella. Furthermore, the investigation on the (UV)-C254 inactivation of the whole bacterial community, in secondary treated wastewater, showed variable UV resistance results. No Salmonella detection was registered at a dose of around 1440 mW s cm-2 since a total disappearance of Salmonella was recorded.
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Affiliation(s)
- Ines Mehri
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Rim Lajnef
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Asma Ben Rejab
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Amel Khessairi
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Hanene Cherif
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Hadda Ouzari
- Laboratoire Microorganisme and Biomolécules Actives, Département de Biologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092, Tunis, Tunisia
| | - Abdennaceur Hassen
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
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11
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Jiao S, Zhang Z, Yang F, Lin Y, Chen W, Wei G. Temporal dynamics of microbial communities in microcosms in response to pollutants. Mol Ecol 2017; 26:923-936. [PMID: 28012222 DOI: 10.1111/mec.13978] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023]
Abstract
Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhengqing Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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12
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Bezza FA, Chirwa EMN. Biosurfactant-Assisted Bioremediation of Polycyclic Aromatic Hydrocarbons (PAHs) in Liquid Culture System and Substrate Interactions. Polycycl Aromat Compd 2016. [DOI: 10.1080/10406638.2015.1129973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Fisseha Andualem Bezza
- Water Utilisation and Environmental Engineering Division, Department of Chemical Engineering, University of Pretoria, Pretoria, Republic of South Africa
| | - Evans M. Nkhalambayausi Chirwa
- Water Utilisation and Environmental Engineering Division, Department of Chemical Engineering, University of Pretoria, Pretoria, Republic of South Africa
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13
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Jiao S, Chen W, Wang E, Wang J, Liu Z, Li Y, Wei G. Microbial succession in response to pollutants in batch-enrichment culture. Sci Rep 2016; 6:21791. [PMID: 26905741 PMCID: PMC4764846 DOI: 10.1038/srep21791] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/29/2022] Open
Abstract
As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México, D.F., Mexico
| | - Junman Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Yining Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
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14
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Sun R, Belcher RW, Liang J, Wang L, Thater B, Crowley DE, Wei G. Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation. J Environ Sci (China) 2015; 33:45-59. [PMID: 26141877 DOI: 10.1016/j.jes.2014.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/23/2014] [Accepted: 11/29/2014] [Indexed: 05/06/2023]
Abstract
Biodegradation of polycyclic aromatic hydrocarbons (PAHs) is normally limited by their low solubility and poor bioavailability. Prior research suggests that biosurfactants are synthesized as intermediates during the production of mucilage at the root tip. To date the effects of mucilage on PAH degradation and microbial community response have not been directly examined. To address this question, our research compared 3 cowpea breeding lines (Vigna unguiculata) that differed in mucilage production for their effects on phenanthrene (PHE) degradation in soil. The High Performance Liquid Chromatography results indicated that the highest PHE degradation rate was achieved in soils planted with mucilage producing cowpea line C1, inoculated with Bradyrhizobium, leading to 91.6% PHE disappearance in 5 weeks. In root printing tests, strings treated with mucilage and bacteria produced larger clearing zones than those produced on mucilage treated strings with no bacteria or bacteria inoculated strings. Experiments with 14C-PHE and purified mucilage in soil slurry confirmed that the root mucilage significantly enhanced PHE mineralization (82.7%), which is 12% more than the control treatment without mucilage. The profiles of the PHE degraders generated by Denaturing gradient gel electrophoresis suggested that cowpea C1, producing a high amount of root mucilage, selectively enriched the PHE degrading bacteria population in rhizosphere. These findings indicate that root mucilage may play a significant role in enhancing PHE degradation and suggests that differences in mucilage production may be an important criterion for selection of the best plant species for use in phytoremediation of PAH contaminated soils.
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Affiliation(s)
- Ran Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. E-mail: .
| | - Richard W Belcher
- Department of Environmental Sciences, University of California at Riverside, Riverside, CA 92521, USA
| | - Jianqiang Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. E-mail:
| | - Li Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. E-mail:
| | - Brian Thater
- Department of Environmental Sciences, University of California at Riverside, Riverside, CA 92521, USA
| | - David E Crowley
- Department of Environmental Sciences, University of California at Riverside, Riverside, CA 92521, USA.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. E-mail: .
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15
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Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation. Appl Microbiol Biotechnol 2015; 99:8751-64. [DOI: 10.1007/s00253-015-6748-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/27/2015] [Accepted: 05/31/2015] [Indexed: 11/25/2022]
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16
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Hydrocarbonoclastic bacteria isolated from petroleum contaminated sites in Tunisia: isolation, identification and characterization of the biotechnological potential. N Biotechnol 2013; 30:723-33. [PMID: 23541698 DOI: 10.1016/j.nbt.2013.03.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/05/2013] [Accepted: 03/13/2013] [Indexed: 11/20/2022]
Abstract
Petroleum hydrocarbons are important energy resources used by industry and in our daily life, whose production contributes highly to environmental pollution. To control such risk, bioremediation constitutes an environmentally friendly alternative technology that has been established and applied. It constitutes the primary mechanism for the elimination of hydrocarbons from contaminated sites by natural existing populations of microorganisms. In this work, a collection of 125 strains, adapted to grow on minimal medium supplemented with crude oil, was obtained from contaminated sediments and seawater from a refinery harbor of the Bizerte coast in the North of Tunisia. The diversity of the bacterial collection was analyzed by amplification of the internal transcribed spacers between the 16S and the 23S rRNA genes (ITS-PCR) and by 16S rRNA sequencing. A total of 36 distinct ITS haplotypes were detected on agarose matrix. Partial 16S rRNA gene sequencing performed on 50 isolates showed high level of identity with known sequences. Strains were affiliated to Ochrabactrum, Sphingobium, Acinetobacter, Gordonia, Microbacterium, Brevundimonas, Novosphingobium, Stenotrophomonas, Luteibacter, Rhodococcus, Agrobacterium, Achromobacter, Bacilllus, Kocuria and Pseudomonas genera. Acinetobacter and Stenotrophomons were found to be the most abundant species characterized by a marked microdiversity as shown through ITS typing. Culture-independent approach (DGGE) showed high diversity in the microbial community in all the studied samples with a clear correlation with the hydrocarbon pollution rate. Sequencing of the DGGE bands revealed a high proportion of Proteobacteria represented by the Alpha and Gamma subclasses. The predominant bacterial detected by both dependent and independent approaches were the Proteobacteria. The biotechnological potential of the isolates revealed a significant production of biosurfactants with important emulsification activities useful in bioremediation. The highest emulsification activity was detected in Pseudomonas geniculata with 52.77% of emulsification. Our overall results suggest that the obtained bacterial isolates may constitute potential candidates for bioremediation and can be useful for biotechnological applications.
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17
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Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol 2012; 8:e1002363. [PMID: 22319433 PMCID: PMC3271020 DOI: 10.1371/journal.pcbi.1002363] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/12/2011] [Indexed: 12/14/2022] Open
Abstract
Microorganisms rarely live isolated in their natural environments but rather function in consolidated and socializing communities. Despite the growing availability of high-throughput sequencing and metagenomic data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of interactions among them. This calls for development of efficient modeling frameworks to shed light on less understood aspects of metabolism in microbial communities. Here, we introduce OptCom, a comprehensive flux balance analysis framework for microbial communities, which relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between individual vs. community level fitness criteria. In contrast to earlier approaches that rely on a single objective function, here, we consider species-level fitness criteria for the inner problems while relying on community-level objective maximization for the outer problem. OptCom is general enough to capture any type of interactions (positive, negative or combinations thereof) and is capable of accommodating any number of microbial species (or guilds) involved. We applied OptCom to quantify the syntrophic association in a well-characterized two-species microbial system, assess the level of sub-optimal growth in phototrophic microbial mats, and elucidate the extent and direction of inter-species metabolite and electron transfer in a model microbial community. We also used OptCom to examine addition of a new member to an existing community. Our study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of various types of interactions in multi-species microbial systems using genome-scale metabolic models.
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Affiliation(s)
- Ali R. Zomorrodi
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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18
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Thomas JC, Dabkowski RT. Glucose and plant exudate enhanced enumeration of bacteria capable of degrading polycyclic aromatic hydrocarbons. Can J Microbiol 2011; 57:1067-72. [DOI: 10.1139/w11-097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enumerating environmental microbial isolates capable of polycyclic aromatic hydrocarbon (PAH) degradation can provide insight into the microbe–plant interactions that facilitate PAH removal. We examined a known PAH degrader ( Pseudomonas putida G7), a nondegrader ( Agrobacterium tumefaciens LBA4404), and several microorganisms isolated from the environment by using a PAH cocktail in an enumeration medium with or without 0.025% (m/v) glucose and (or) root exudates. Compared with the standard most probable number (MPN), the addition of glucose and root exudates in a modified MPN method resulted in a 3- to 11-fold enhancement of PAH degraders being enumerated among microorganisms found in PAH-contaminated soils. High-performance liquid chromatography analysis verified that PAH levels were reduced using this modified enumeration method. Low levels of glucose, perhaps in concert with other materials in exudates, may promote microbial metabolism, thereby enhancing PAH degradation.
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Affiliation(s)
- John C. Thomas
- University of Michigan-Dearborn Department of Natural Sciences, 4901 Evergreen Road, Dearborn, MI 48128-1491, USA
| | - Robert T. Dabkowski
- University of Michigan-Dearborn Department of Natural Sciences, 4901 Evergreen Road, Dearborn, MI 48128-1491, USA
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19
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Morimoto S, Ogawa N, Hasebe A, Fujii T. Isolation of effective 3-chlorobenzoate-degraders in soil using community analyses by PCR-DGGE. Microbes Environ 2011; 23:285-92. [PMID: 21558720 DOI: 10.1264/jsme2.me08526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The screening of pollutant degraders by relying solely on cultivation techniques such as liquid enrichment often fails to isolate the actual degraders in the environment. Community analyses by PCR-denaturing gradient gel electrophoresis (DGGE) were performed to isolate bacteria that can degrade 3-chlorobenzoate (3CB) effectively in soil. A forest soil sample was repeatedly dosed with 3CB (500 mg kg(-1)) to enrich it with indigenous 3CB-degraders, and changes in the bacterial community were monitored by PCR-DGGE of the 16S rRNA gene and benzoate 1,2-dioxygenase alpha subunit gene (benA). Initially, it required about 3 weeks to degrade 3CB in the soil, whereas it took only 3 days after the third dose. With this accelerated degradation, several intensified bands appeared in the DGGE profiles of both 16S rRNA gene and benA. We succeeded in isolating five 3CB-degrading Burkholderia strains corresponding to these bands by direct plating, while most of them were eliminated by liquid enrichment. Inoculation of the strains into the soil demonstrated that the five strains could degrade 3CB effectively in the soil. This study clearly shows significant bias during the liquid enrichment process and the advantage of using PCR-DGGE in screening effective degraders under environmental conditions.
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Affiliation(s)
- Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3-1-3 Kannodai, Tsukuba, Ibaraki 305-9604, Japan
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20
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Wang YF, Tam NFY. Microbial community dynamics and biodegradation of polycyclic aromatic hydrocarbons in polluted marine sediments in Hong Kong. MARINE POLLUTION BULLETIN 2011; 63:424-430. [PMID: 21620420 DOI: 10.1016/j.marpolbul.2011.04.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 04/29/2011] [Accepted: 04/30/2011] [Indexed: 05/30/2023]
Abstract
Dynamics of microbial community and biodegradation of polycyclic aromatic hydrocarbons (PAHs) in polluted marine sediments, artificially spiked with a mixture of PAHs (fluorene, phenanthrene, fluoranthene and pyrene), were examined for a period of 60 days. Microbial communities were characterised by bacterial counts, ester-linked fatty acid methyl ester (EL-FAME) analysis and denaturing gradient gel electrophoresis (DGGE). A noted reduction in species diversity occurred only in the high PAH level treatment at onset. Both EL-FAME and DGGE demonstrated a marked shift in microbial community, in all the PAH level treatments, afterwards, with increases in the number of fatty acid degraders, the relative abundance of fatty acid biomarkers for gram-negative bacteria and a decrease in species diversity. The shift was also accompanied by the significant decrease in PAH concentrations. By the end of the experiment, diversity indices, based on both approaches, recovered when PAH concentrations declined to their background levels, except in the high PAH level treatment.
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Affiliation(s)
- Y F Wang
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
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21
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Miller LD, Mosher JJ, Venkateswaran A, Yang ZK, Palumbo AV, Phelps TJ, Podar M, Schadt CW, Keller M. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiol 2010; 10:149. [PMID: 20497531 PMCID: PMC2906461 DOI: 10.1186/1471-2180-10-149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 05/24/2010] [Indexed: 01/03/2023] Open
Abstract
Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.
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Affiliation(s)
- Lance D Miller
- Biosciences and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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22
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Isaza PA, Daugulis AJ. Enhanced degradation of phenanthrene in a solid-liquid two-phase partitioning bioreactor via sonication. Biotechnol Bioeng 2010; 105:997-1001. [PMID: 19998286 DOI: 10.1002/bit.22618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The current article examined the feasibility of inducing improved delivery and degradation of phenanthrene in a solid-liquid partitioning bioreactor system at bench scale by means of ultrasonic energy input. Initial degradation rates of phenanthrene by a microbial consortium, delivered from Desmopan, were improved 2.7-fold in the presence of sonication relative to unsonicated controls. Results demonstrated that an operating window involving on/off sonication cycling improved substrate delivery and rational selection of ultrasound cycling profiles could lead to even further enhancements. Additionally, all results were obtained in a conventional bioreactor with commercial ultrasonic equipment and a commercially available polymer. Subsequent DGGE analysis demonstrated that the sonication cycles selected maintained consortium compositions, relative to control cases, and suggest that exposure would not reduce degradative capabilities under the periods of irradiation examined. Finally, consortium members were identified as belonging to the Pandoraea, Sphingobium, and Pseudoxanthomonas genera. Comparison of genetic sequences in the Ribosomal Database Project revealed that some of the bacterial members, identified at the strain level, had been previously observed in PAH degradations, while others have been reported only in the degradation of other aromatics, such as pesticides.
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Affiliation(s)
- Pedro A Isaza
- Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada
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Biodegradation: gaining insight through proteomics. Biodegradation 2010; 21:861-79. [DOI: 10.1007/s10532-010-9361-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
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Kanaly RA, Harayama S. Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 2010; 3:136-64. [PMID: 21255317 PMCID: PMC3836582 DOI: 10.1111/j.1751-7915.2009.00130.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/22/2009] [Accepted: 05/26/2009] [Indexed: 11/26/2022] Open
Abstract
Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.
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Affiliation(s)
- Robert A Kanaly
- Department of Genome Systems, Faculty of Bionanoscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Kanagawa-ken, Yokohama 236-0027, Japan.
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Sun R, Jin J, Sun G, Liu Y, Liu Z. Screening and degrading characteristics and community structure of a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterial consortium from contaminated soil. J Environ Sci (China) 2010; 22:1576-1585. [PMID: 21235189 DOI: 10.1016/s1001-0742(09)60292-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Inoculation with efficient microbes had been proved to be the most important way for the bioremediation of polluted environments. For the treatment of abandoned site of Beijing Coking Chemical Plant contaminated with high level of high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs), a bacterial consortium capable of degrading HMW-PAHs, designated 1-18-1, was enriched and screened from HMW-PAHs contaminated soil. Its degrading ability was analyzed by high performance liquid chromatography (HPLC), and the community structure was investigated by construction and analyses of the 16S rRNA gene clone libraries (A, B and F) at different transfers. The results indicated that 1-18-1 was able to utilize pyrene, fluoranthene and benzo[a]pyrene as sole carbon and energy source for growth. The degradation rate of pyrene and fluoranthene reached 82.8% and 96.2% after incubation for 8 days at 30 degrees C, respectively; while the degradation rate of benzo[a]pyrene was only 65.1% after incubation for 28 days at 30 degrees C. Totally, 108, 100 and 100 valid clones were randomly selected and sequenced from the libraries A, B, and F. Phylogenetic analyses showed that all the clones could be divided into 5 groups, Bacteroidetes, alpha-Proteobacteria, Actinobacteria, beta-Proteobacteria and gamma-Proteobacteria. Sequence similarity analyses showed total 39 operational taxonomic units (OTUs) in the libraries. The predominant bacterial groups were alpha-Proteobacteria (19 OTUs, 48.7%), gamma-Proteobacteria (9 OTUs, 23.1%) and beta-Proteobacteria (8 OTUs, 20.5%). During the transfer process, the proportions of alpha-Proteobacteria and beta-Proteobacteria increased greatly (from 47% to 93%), while gamma-Proteobacteria decreased from 32% (library A) to 6% (library F); and Bacteroidetes group disappeared in libraries B and F.
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Affiliation(s)
- Run Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Optimized PCR-Temporal Temperature Gel Electrophoresis compared to cultivation to assess diversity of gut microbiota in neonates. J Microbiol Methods 2009; 79:156-65. [DOI: 10.1016/j.mimet.2009.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/06/2009] [Accepted: 08/06/2009] [Indexed: 11/22/2022]
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Isolation and genetic identification of PAH degrading bacteria from a microbial consortium. Biodegradation 2009; 20:789-800. [DOI: 10.1007/s10532-009-9267-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
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Lafortune I, Juteau P, Déziel E, Lépine F, Beaudet R, Villemur R. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem. MICROBIAL ECOLOGY 2009; 57:455-468. [PMID: 18615233 DOI: 10.1007/s00248-008-9417-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 06/05/2008] [Indexed: 05/26/2023]
Abstract
High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty-five percent of clones and strains were affiliated to Alphaproteobacteria and Betaproteobacteria; among them, several were affiliated to bacterial species known for their PAH degradation activities such as those belonging to the Sphingomonadaceae. Finally, three genes involved in the degradation of aromatic molecules were detected in the consortium and two in IAFILS9. This study provides information on the bacterial composition of a HWM PAH-degrading consortium and its dynamics in a TLP biosystem during PAH degradation.
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Lladó S, Jiménez N, Viñas M, Solanas AM. Microbial populations related to PAH biodegradation in an aged biostimulated creosote-contaminated soil. Biodegradation 2009; 20:593-601. [PMID: 19153811 DOI: 10.1007/s10532-009-9247-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 01/06/2009] [Indexed: 11/26/2022]
Abstract
A previous bioremediation survey on a creosote-contaminated soil showed that aeration and optimal humidity promoted depletion of three-ringed polycyclic aromatic hydrocarbons (PAHs), but residual concentrations of four-ringed benzo(a)anthracene (B(a)A) and chrysene (Chry) remained. In order to explain the lack of further degradation of heavier PAHs such as four-ringed PAHs and to analyze the microbial population responsible for PAH biodegradation, a chemical and microbial molecular approach was used. Using a slurry incubation strategy, soil in liquid mineral medium with and without additional B(a)A and Chry was found to contain a powerful PAH-degrading microbial community that eliminated 89% and 53% of the added B(a)A and Chry, respectively. It is hypothesized that the lack of PAH bioavailability hampered their further biodegradation in the unspiked soil. According to the results of the culture-dependent and independent techniques Mycobacterium parmense, Pseudomonas mexicana, and Sphingobacterials group could control B(a)A and Chry degradation in combination with several microorganisms with secondary metabolic activity.
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Affiliation(s)
- Salvador Lladó
- Department of Microbiology, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain
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Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl Environ Microbiol 2008; 74:7313-20. [PMID: 18835999 DOI: 10.1128/aem.01695-08] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A bacterium designated strain BD-a59, able to degrade all six benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) compounds, was isolated by plating gasoline-contaminated sediment from a gasoline station in Geoje, Republic of Korea, without enrichment, on minimal salts basal (MSB) agar containing 0.01% yeast extract, with BTEX as the sole carbon and energy source. Taxonomic analyses showed that the isolate belonged to Pseudoxanthomonas spadix, and until now, the genus Pseudoxanthomonas has not included any known BTEX degraders. The BTEX biodegradation rate was very low in MSB broth, but adding a small amount of yeast extract greatly enhanced the biodegradation. Interestingly, degradation occurred very quickly in slurry systems amended with sterile soil solids but not with aqueous soil extract. Moreover, if soil was combusted first to remove organic matter, the enhancement effect on BTEX biodegradation was lost, indicating that some components of insoluble organic compounds are nutritionally beneficial for BTEX degradation. Reverse transcriptase PCR-based analysis of field-fixed mRNA revealed expression of the tmoA gene, whose sequence was closely related to that carried by strain BD-a59. This study suggests that strain BD-a59 has the potential to assist in BTEX biodegradation at contaminated sites.
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Grant RJ, Muckian LM, Clipson NJW, Doyle EM. Microbial community changes during the bioremediation of creosote-contaminated soil. Lett Appl Microbiol 2007; 44:293-300. [PMID: 17309507 DOI: 10.1111/j.1472-765x.2006.02066.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To investigate the effects of aeration on the ex situ biodegradation of polycyclic aromatic hydrocarbons (PAHs) in creosote-contaminated soil and its effect on the microbial community present. METHODS AND RESULTS Aerated and nonaerated microcosms of soil excavated from a former timber treatment yard were maintained and sampled for PAH concentration and microbial community changes by terminal restriction fragment length polymorphism (TRFLP) analysis. After an experimental period of just 13 days, degradation was observed with all the PAHs monitored. Abiotic controls showed no loss of PAH. Results unexpectedly showed greater loss of the higher molecular weight PAHs in the nonaerated control. This may have been due to the soil excavation causing initial decompaction and aeration and the resulting changes caused in the microbial community composition, indicated by TRFLP analysis showing several ribotypes greatly increasing in relative abundance. Similar changes in both microcosms were observed but with several possible key differences. The species of micro-organisms putatively identified included Bacilli, pseudomonad, aeromonad, Vibrio and Clostridia species. CONCLUSIONS Excavation of the contaminated soil leads to decompaction, aeration and increased nutrient availability, which in turn allow microbial biodegradation of the PAHs and a change in the microbial community structure. SIGNIFICANCE AND IMPACT OF THE STUDY Understanding the changes occurring in the microbial community during biodegradation of all PAHs is essential for the development of improved site remediation protocols. TRFLP allows useful monitoring of the total microbial community.
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Affiliation(s)
- R J Grant
- School of Biological and Environmental Science, University College Dublin, Dublin 4, Ireland.
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Ozaki S, Kishimoto N, Fujita T. Change in the Predominant Bacteria in a Microbial Consortium Cultured on Media Containing Aromatic and Saturated Hydrocarbons as the Sole Carbon Source. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shingen Ozaki
- Graduate School of Applied Biological Chemistry, Kinki University
| | | | - Tokio Fujita
- Graduate School of Applied Biological Chemistry, Kinki University
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Viñas M, Sabaté J, Espuny MJ, Solanas AM. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 2005; 71:7008-18. [PMID: 16269736 PMCID: PMC1287751 DOI: 10.1128/aem.71.11.7008-7018.2005] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the alpha-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the gamma-Proteobacteria group (genus Xanthomonas), the alpha-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the gamma-Proteobacteria group (genus Xathomonas), the beta-Proteobacteria group (genera Alcaligenes and Achromobacter), and the alpha-Proteobacteria group (genus Sphingomonas) were the dominant groups in the nutrient treatment. This study shows that specific bacterial phylotypes are associated both with different phases of PAH degradation and with nutrient addition in a preadapted PAH-contaminated soil. Our findings also suggest that there are complex interactions between bacterial species and medium conditions that influence the biodegradation capacity of the microbial communities involved in bioremediation processes.
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Affiliation(s)
- Marc Viñas
- Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
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