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Wang Y, Li A, Zou B, Qian Y, Li X, Sun Z. The Combination of Buchloe dactyloides Engelm and Biochar Promotes the Remediation of Soil Contaminated with Polycyclic Aromatic Hydrocarbons. Microorganisms 2024; 12:968. [PMID: 38792797 PMCID: PMC11124401 DOI: 10.3390/microorganisms12050968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (streptomyces, curvularia, mortierella and acremonium) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.
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Affiliation(s)
- Yuancheng Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.W.); (A.L.)
| | - Ao Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.W.); (A.L.)
| | - Bokun Zou
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; (B.Z.); (Y.Q.)
| | - Yongqiang Qian
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; (B.Z.); (Y.Q.)
| | - Xiaoxia Li
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; (B.Z.); (Y.Q.)
| | - Zhenyuan Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.W.); (A.L.)
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Min Z, Rui T, Yu L. A combination of microbial electrolysis cells and bioaugmentation can effectively treat synthetic wastewater containing polycyclic aromatic hydrocarbon. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:2716-2731. [PMID: 38822610 DOI: 10.2166/wst.2024.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024]
Abstract
The anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) is challenging due to its toxic effect on the microbes. Microbial electrolysis cells (MECs), with their excellent characteristics of anodic and cathodic biofilms, can be a viable way to enhance the biodegradation of PAHs. This work assessed different cathode materials (carbon brush and nickel foam) combined with bioaugmentation on typical PAHs-naphthalene biodegradation and analyzed the inhibition amendment mechanism of microbial biofilms in MECs. Compared with the control, the degradation efficiency of naphthalene with the nickel foam cathode supplied with bioaugmentation dosage realized a maximum removal rate of 94.5 ± 3.2%. The highest daily recovered methane yield (227 ± 2 mL/gCOD) was also found in the nickel foam cathode supplied with bioaugmentation. Moreover, the microbial analysis demonstrated the significant switch of predominant PAH-degrading microorganisms from Pseudomonas in control to norank_f_Prolixibacteraceae in MECs. Furthermore, hydrogentrophic methanogenesis prevailed in MEC reactors, which is responsible for methane production. This study proved that MEC combined with bioaugmentation could effectively alleviate the inhibition of PAH, with the nickel foam cathode obtaining the fastest recovery rate in terms of methane yield.
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Affiliation(s)
- Zhang Min
- College of Engineering, China Agricultural University (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), Beijing 100083, China
| | - Tang Rui
- College of Engineering, China Agricultural University (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), Beijing 100083, China
| | - Li Yu
- College of Engineering, China Agricultural University (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), Beijing 100083, China E-mail:
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Dong S, Yan PF, Mezzari MP, Abriola LM, Pennell KD, Cápiro NL. Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7480-7492. [PMID: 38639388 DOI: 10.1021/acs.est.4c00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Microbial transformation of per- and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.
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Affiliation(s)
- Sheng Dong
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
| | - Peng-Fei Yan
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
| | - Melissa P Mezzari
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Linda M Abriola
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Natalie L Cápiro
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
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DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation. Sci Rep 2022; 12:19232. [PMID: 36357494 PMCID: PMC9649793 DOI: 10.1038/s41598-022-23728-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant-microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.
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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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Zhang Z, Guo H, Sun J, Gong X, Wang C, Wang H. Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149148. [PMID: 34311378 DOI: 10.1016/j.scitotenv.2021.149148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [13C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO3-, phenanthrene+H13CO3-, and [D10]-phenanthrene+HCO3- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.
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Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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7
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Wang YQ, Wang MX, Chen YY, Li CM, Zhou ZF. Microbial community structure and co-occurrence are essential for methanogenesis and its contribution to phenanthrene degradation in paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126086. [PMID: 34020358 DOI: 10.1016/j.jhazmat.2021.126086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Although polycyclic aromatic hydrocarbons (PAHs) degradation under methanogenesis is an ideal approach to remediating PAH-polluted soil, the contribution of methanogenesis to soil PAH elimination and the relationships between microbial ecological characteristics and PAH degradation during this process remain unclear. Here, we conducted a short-term (60 days) incubation using a paddy soil amended with phenanthrene and examined the effects of a specific methanogenic inhibitor (2-bromoethanesulfonate, BES) on this process. As treatment assessments, the methane production activity (MPA), phenanthrene degradation rate (PDR), and microbial ecological characteristics were determined. The results indicated that BES significantly inhibited both soil MPA and PDR, and we detected a positive relationship between MPA and PDR. Furthermore, BES significantly altered the soil microbial community structure, and it was the microbial community structure but not α-diversity was significantly correlated with soil MPA and PDR. BES decentralized the co-occurrence of bacterial genera but intensified the co-occurrence of methanogens. Moreover, certain bacterial taxa, including Bacteroidetes-vadinHA17, Gemmatimonas, and Sporomusaceae, were responsible for the MPA and PDR in this paddy soil. Collectively, these findings confirm the role of methanogenesis in PAH elimination from paddy soil, and reveal the importance of microbial co-occurrence characteristics in the determination of soil MPA and pollutant metabolism.
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Affiliation(s)
- Yan-Qin Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ming-Xia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Yong-Yi Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chun-Ming Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhi-Feng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China
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Sengupta K, Pal S. A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40288-40307. [PMID: 33844144 DOI: 10.1007/s11356-021-13666-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.
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Affiliation(s)
- Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Pune, 411004, India
| | - Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
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Rajbongshi A, Gogoi SB. A review on anaerobic microorganisms isolated from oil reservoirs. World J Microbiol Biotechnol 2021; 37:111. [PMID: 34076736 DOI: 10.1007/s11274-021-03080-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H2S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.
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Affiliation(s)
- Amarjit Rajbongshi
- Brahmaputra Valley Fertilizer Corporation Limited, Namrup, Assam, India.
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10
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Wang B, Teng Y, Yao H, Christie P. Detection of functional microorganisms in benzene [a] pyrene-contaminated soils using DNA-SIP technology. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124788. [PMID: 33321373 DOI: 10.1016/j.jhazmat.2020.124788] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
DNA-SIP technology was used to detect active BaP-degraders involved in the biodegradation of benzo [a] pyrene (BaP) in two soils separately and in mixture. The lowest BaP removal was observed in red soil, and Ramlibacter (OTU830) belonging to the γ-Proteobacteria was labeled as BaP degrader with 13C-BaP. The highest diversity of degrading microorganisms occurred in the paddy soil with OTUs belonging to Nocardioids, Micromonospora, Saccharothrix, Lysobacter and Methylium present and a BaP removal efficiency of 29.5% after 14 d. BaP degraders in the mixed microbiome of the soil mixture were Burkholderia and Phenylobacterium, together with Nocardioides and Micromonospora as in the paddy soil. These results indicated that the active BaP-degraders in the mixed microbiome were identical to the active BaP-degraders in paddy soil (OTU356 and OTU328), but also unique in the mixed microbiome, such as OTU393 and OTU392. The functional genes of PAH-ring hydroxylating dioxygenases (PAH-RHDα) were expressed and were positively related to the removal of BaP, and the active BaP degrading bacteria included both Gram-positive and Gram-negative bacteria. Saccharothrix, Phylobacterium, Micromonospora and Nocardioids are here reported as BaP degraders for the first time using DNA-SIP.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environmental Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Huaiying Yao
- Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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11
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Dhar K, Subashchandrabose SR, Venkateswarlu K, Krishnan K, Megharaj M. Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 251:25-108. [PMID: 31011832 DOI: 10.1007/398_2019_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.
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Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, India
| | - Kannan Krishnan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia.
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12
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Ye Q, Liang C, Chen X, Fang T, Wang Y, Wang H. Molecular characterization of methanogenic microbial communities for degrading various types of polycyclic aromatic hydrocarbon. J Environ Sci (China) 2019; 86:97-106. [PMID: 31787194 DOI: 10.1016/j.jes.2019.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 06/10/2023]
Abstract
Knowledge on methanogenic microbial communities associated with the degradation of polycyclic aromatic hydrocarbons (PAHs) is crucial to developing strategies for PAHs bioremediation. In this study, the linkage between the type of PAHs and microbial community structure was fully investigated through 16S rRNA gene sequencing on four PAH-degrading cultures. Putative degradation products were also detected. Our results indicated that naphthalene (Nap)/2-methylnaphthalene (2-Nap), phenanthrene (Phe) and anthracene (Ant) sculpted different microbial communities. Among them, Nap and 2-Nap selected for similar degrading bacteria (i.e., Alicycliphilus and Thauera) and methanogens (Methanomethylovorans and Methanobacterium). Nap and 2-Nap were probably activated via carboxylation, producing 2-naphthoic acid. In contrast, Phe and Ant shaped different bacterial and archaeal communities, with Arcobacter and Acinetobacter being Phe-degraders and Thiobacillus Ant-degrader. Methanogenic archaea Methanobacterium and Methanomethylovorans predominated Phe-degrading and Ant-degrading culture, respectively. These findings can improve our understanding of natural PAHs attenuation and provide some guidance for PAHs bioremediation in methanogenic environment.
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Affiliation(s)
- Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Chengyue Liang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xunwen Chen
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tingting Fang
- 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
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Thomas F, Corre E, Cébron A. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. THE ISME JOURNAL 2019; 13:1814-1830. [PMID: 30872807 PMCID: PMC6775975 DOI: 10.1038/s41396-019-0394-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.
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Affiliation(s)
- François Thomas
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France.
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Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms 2018; 6:microorganisms6030065. [PMID: 29996505 PMCID: PMC6164631 DOI: 10.3390/microorganisms6030065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 11/23/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.
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15
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Song M, Jiang L, Zhang D, Luo C, Wang Y, Yu Z, Yin H, Zhang G. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 308:50-57. [PMID: 26808242 DOI: 10.1016/j.jhazmat.2016.01.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.
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Affiliation(s)
- Mengke Song
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Longfei Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Yan Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Yu
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Hua Yin
- College of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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16
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Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
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17
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Vogt C, Lueders T, Richnow HH, Krüger M, von Bergen M, Seifert J. Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders. J Mol Microbiol Biotechnol 2016; 26:195-210. [DOI: 10.1159/000440806] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using <sup>13</sup>C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.
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Jiménez N, Richnow HH, Vogt C, Treude T, Krüger M. Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies. J Mol Microbiol Biotechnol 2016; 26:227-42. [PMID: 26959375 DOI: 10.1159/000441679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.
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Affiliation(s)
- Núria Jiménez
- Department of Resource Geochemistry, BGR - Federal Institute for Geosciences and Natural Resources, Hannover, Germany
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19
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Ladino-Orjuela G, Gomes E, da Silva R, Salt C, Parsons JR. Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 237:105-121. [PMID: 26613990 DOI: 10.1007/978-3-319-23573-8_5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.
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Affiliation(s)
- Guillermo Ladino-Orjuela
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Eleni Gomes
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Roberto da Silva
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Christopher Salt
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
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Identification of benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing. Appl Environ Microbiol 2015; 81:7368-76. [PMID: 26253666 DOI: 10.1128/aem.01983-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/02/2015] [Indexed: 01/21/2023] Open
Abstract
DNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genus Terrimonas (family Chitinophagaceae, order Sphingobacteriales), whereas Burkholderia spp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the family Oxalobacteraceae (genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP (13)C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils.
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Braun F, Hamelin J, Bonnafous A, Delgenès N, Steyer JP, Patureau D. Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane. PLoS One 2015; 10:e0125552. [PMID: 25874750 PMCID: PMC4398385 DOI: 10.1371/journal.pone.0125552] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/25/2015] [Indexed: 02/01/2023] Open
Abstract
Urban sludge produced on wastewater treatment plants are often contaminated by organic pollutants such as polycyclic aromatic hydrocarbons (PAH). Their removal under methanogenic conditions was already reported, but the factors influencing this removal remain unclear. Here, we determined the influence of microbial communities on PAH removal under controlled physico-chemical conditions. Twelve mesophilic anaerobic digesters were inoculated with three microbial communities extracted from ecosystems with contrasting pollution histories: a PAH contaminated soil, a PCB contaminated sediment and a low contaminated anaerobic sludge. These anaerobic digesters were operated during 100 days in continuous mode. A sterilised activated sludge, spiked with 13 PAH at concentrations usually encountered in full-scale wastewater treatment plants, was used as substrate. The dry matter and volatile solid degradation, the biogas production rate and composition, the volatile fatty acids (VFA) production and the PAH removals were monitored. Bacterial and archaeal communities were compared in abundance (qPCR), in community structure (SSCP fingerprinting) and in dominant microbial species (454-pyrosequencing). The bioreactors inoculated with the community extracted from low contaminated anaerobic sludge showed the greater methane production. The PAH removals ranged from 10 % to 30 %, respectively, for high and low molecular weight PAH, whatever the inoculums tested, and were highly correlated with the dry matter and volatile solid removals. The microbial community structure and diversity differed with the inoculum source; this difference was maintained after the 100 days of digestion. However, the PAH removal was not correlated to these diverse structures and diversities. We hence obtained three functional stable consortia with two contrasted metabolic activities, and three different pictures of microbial diversity, but similar PAH and matter removals. These results confirm that PAH removal depends on the molecule type and on the solid matter removal. But, as PAH elimination is similar whether the solid substrate is degraded into VFA or into methane, it seems that the fermentative communities are responsible for their elimination.
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Affiliation(s)
- Florence Braun
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
- ADEME, French Environment and Energy Management Agency, 20 avenue du Grésillé-BP 90406, F-49004, Angers, Cedex 01, France
| | - Jérôme Hamelin
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Anaïs Bonnafous
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Nadine Delgenès
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Jean-Philippe Steyer
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Dominique Patureau
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
- * E-mail:
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23
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Wang Z, Yang Y, Sun W, Dai Y, Xie S. Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:2342-2349. [PMID: 25277711 DOI: 10.1007/s11356-014-3625-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.
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Affiliation(s)
- Zhao Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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24
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Liao X, Chen C, Zhang J, Dai Y, Zhang X, Xie S. Dimethylamine biodegradation by mixed culture enriched from drinking water biofilter. CHEMOSPHERE 2015; 119:935-940. [PMID: 25280176 DOI: 10.1016/j.chemosphere.2014.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/26/2014] [Accepted: 09/05/2014] [Indexed: 06/03/2023]
Abstract
Dimethylamine (DMA) is one of the important precursors of drinking water disinfection by-product N-nitrosodimethylamine (NDMA). Reduction of DMA to minimize the formation of carcinogenic NDMA in drinking water is of practical importance. Biodegradation plays a major role in elimination of DMA pollution in the environment, yet information on DMA removal by drinking water biofilter is still lacking. In this study, microcosms with different treatments were constructed to investigate the potential of DMA removal by a mixed culture enriched from a drinking water biofilter and the effects of carbon and nitrogen sources. DMA could be quickly mineralized by the enrichment culture. Amendment of a carbon source, instead of a nitrogen source, had a profound impact on DMA removal. A shift in bacterial community structure was observed with DMA biodegradation, affected by carbon and nitrogen sources. Proteobacteria was the predominant phylum group in DMA-degrading microcosms. Microorganisms from a variety of bacterial genera might be responsible for the rapid DMA mineralization.
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Affiliation(s)
- Xiaobin Liao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chao Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiaojian Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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25
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Yang Y, Wang J, Liao J, Xie S, Huang Y. Distribution of naphthalene dioxygenase genes in crude oil-contaminated soils. MICROBIAL ECOLOGY 2014; 68:785-793. [PMID: 25008984 DOI: 10.1007/s00248-014-0457-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are one of the major pollutants in soils in oil exploring areas. Biodegradation is the major process for natural elimination of PAHs from contaminated soils. Functional genes can be used as biomarkers to assess the biodegradation potential of indigenous microbial populations. However, little is known about the distribution of PAH-degrading genes in the environment. The links between environmental parameters and the distribution of PAH metabolic genes remain essentially unclear. The present study investigated the abundance and diversity of naphthalene dioxygenase genes in the oil-contaminated soils in the Shengli Oil Field (China). Spatial variations in the density and diversity of naphthalene dioxygenase genes occurred in this area. Four different sequence genotypes were observed in the contaminated soils, with the predominance of novel PAH-degrading genes. Pearson's correlation analysis illustrated that gene abundance had positive correlations with the levels of total organic carbon and aromatic hydrocarbons, while gene diversity showed a negative correlation with the level of polar aromatics. This work could provide some new insights toward the distribution of PAH metabolic genes and PAH biodegradation potential in oil-contaminated ecosystems.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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Wang Z, Yang Y, Sun W, Xie S, Liu Y. Nonylphenol biodegradation in river sediment and associated shifts in community structures of bacteria and ammonia-oxidizing microorganisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 106:1-5. [PMID: 24836870 DOI: 10.1016/j.ecoenv.2014.04.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/17/2014] [Accepted: 04/19/2014] [Indexed: 06/03/2023]
Abstract
Nonylphenol (NP) is one of commonly detected contaminants in the environment. Biological degradation is mainly responsible for remediation of NP-contaminated site. Knowledge about the structure of NP-degrading microbial community is still very limited. Microcosms were constructed to investigate the structure of microbial community in NP-contaminated river sediment and its change with NP biodegradation. A high level of NP was significantly dissipated in 6-9 days. Bacteria and ammonia-oxidizing archaea (AOA) were more responsive to NP amendment compared to ammonia-oxidizing bacteria (AOB). Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes were the largest bacterial groups in NP-degrading sediment. Microorganisms from bacterial genera Brevundimonas, Flavobacterium, Lysobacter and Rhodobacter might be involved in NP degradation in river sediment. This study provides some new insights towards NP biodegradation and microbial ecology in NP-contaminated environment.
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Affiliation(s)
- Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Yuyin Yang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Weimin Sun
- Department of Environmental Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
| | - Yong Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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Gieg LM, Fowler SJ, Berdugo-Clavijo C. Syntrophic biodegradation of hydrocarbon contaminants. Curr Opin Biotechnol 2014; 27:21-9. [DOI: 10.1016/j.copbio.2013.09.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
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Berdugo-Clavijo C, Gieg LM. Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters. Front Microbiol 2014; 5:197. [PMID: 24829563 PMCID: PMC4017130 DOI: 10.3389/fmicb.2014.00197] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/14/2014] [Indexed: 11/13/2022] Open
Abstract
The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir.
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Affiliation(s)
| | - Lisa M. Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of CalgaryCalgary, AB, Canada
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Wan R, Wang Z, Xie S. Dynamics of communities of bacteria and ammonia-oxidizing microorganisms in response to simazine attenuation in agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 472:502-508. [PMID: 24317158 DOI: 10.1016/j.scitotenv.2013.11.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 06/02/2023]
Abstract
Autochthonous microbiota plays a crucial role in natural attenuation of s-triazine herbicides in agricultural soil. Soil microcosm study was carried out to investigate the shift in the structures of soil autochthonous microbial communities and the potential degraders associated with natural simazine attenuation. The relative abundance of soil autochthonous degraders and the structures of microbial communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. Phylogenetic composition of bacterial community was also characterized using clone library analysis. Soil autochthonous microbiota could almost completely clean up simazine (100 mg kg(-1)) in 10 days after herbicide application, indicating a strong self-remediation potential of agricultural soil. A significant increase in the proportion of s-triazine-degrading atzC gene was found in 6 days after simazine amendment. Simazine application could alter the community structures of total bacteria and ammonia-oxidizing archaea (AOA) and bacteria (AOB). AOA were more responsive to simazine application compared to AOB and bacteria. Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were the dominant bacterial groups either at the initial stage after simazine amendment or at the end stage of herbicide biodegradation, but Actinobacteria predominated at the middle stage of biodegradation. Microorganisms from several bacterial genera might be involved in simazine biodegradation. This work could add some new insights on the bioremediation of herbicides contaminated agricultural soils.
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Affiliation(s)
- Rui Wan
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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30
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Yang Y, Wang Z, Xie S. Aerobic biodegradation of bisphenol A in river sediment and associated bacterial community change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 470-471:1184-1188. [PMID: 24246941 DOI: 10.1016/j.scitotenv.2013.10.102] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/25/2013] [Accepted: 10/27/2013] [Indexed: 06/02/2023]
Abstract
Bisphenol A (BPA) is one of the commonly detected endocrine-disrupting chemicals in the environment. Biodegradation plays a major role in elimination of BPA pollution in the environment. However, information on the structure of BPA-degrading microbial community is still lacking. In this study, microcosms with different treatments were constructed to investigate the microbial community structure in river sediment and its shift during BPA biodegradation. BPA could be quickly depleted in the BPA-spiked sediment. BPA amendment had a significant impact on sediment bacterial community, influenced by dosage levels. Gammaproteobacteria and Alphaproteobacteria were the predominant bacterial groups in BPA-degrading sediment microcosm. A consortium of microorganisms from different bacterial genera might be involved in BPA biodegradation in river sediment. This study provides some new insights towards BPA biodegradation and microbial ecology in BPA-degrading environment.
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Affiliation(s)
- Yuyin Yang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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Dunlevy SR, Singleton DR, Aitken MD. Biostimulation Reveals Functional Redundancy of Anthracene-Degrading Bacteria in Polycyclic Aromatic Hydrocarbon-Contaminated Soil. ENVIRONMENTAL ENGINEERING SCIENCE 2013; 30:697-705. [PMID: 24302851 PMCID: PMC3833303 DOI: 10.1089/ees.2013.0067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/28/2013] [Indexed: 05/25/2023]
Abstract
Stable-isotope probing was previously used to identify bacterial anthracene-degraders in untreated soil from a former manufactured gas plant site. However, subsequent pyrosequence analyses of total bacterial communities and quantification of 16S rRNA genes indicated that relative abundances of the predominant anthracene-degrading bacteria (designated Anthracene Group 1) diminished as a result of biological treatment conditions in lab-scale, aerobic bioreactors. This study identified Alphaproteobacterial anthracene-degrading bacteria in bioreactor-treated soil which were dissimilar to those previously identified. The largest group of sequences was from the Alterythrobacter genus while other groups of sequences were associated with bacteria within the order Rhizobiales and the genus Bradyrhizobium. Conditions in the bioreactor enriched for organisms capable of degrading anthracene which were not the same as those identified as dominant degraders in the untreated soil. Further, these data suggest that identification of polycyclic aromatic hydrocarbon-degrading bacteria in contaminated but untreated soil may be a poor indicator of the most active degraders during biological treatment.
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Affiliation(s)
| | - David R. Singleton
- Corresponding author: David R. Singleton, Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Room 0030 Michael Hooker Research Center, Chapel Hill, NC 27599-7431. Phone: 1-919-966-5452; Fax: 1-919-966-7911; E-mail:
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Xie S, Wan R, Wang Z, Wang Q. Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:4078-4084. [PMID: 23224504 DOI: 10.1007/s11356-012-1356-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain's survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain's trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.
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Affiliation(s)
- Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing, 100871, China.
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Zhou X, Wang Q, Wang Z, Xie S. Nitrogen impacts on atrazine-degrading Arthrobacter strain and bacterial community structure in soil microcosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:2484-2491. [PMID: 22961491 DOI: 10.1007/s11356-012-1168-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 08/27/2012] [Indexed: 06/01/2023]
Abstract
The objective of this study was to investigate the impacts of exogenous nitrogen on a microbial community inoculated with the atrazine-degrading Arthrobacter sp. in soil amended with a high concentration of atrazine. Inoculated and uninoculated microcosms for biodegradation tests were constructed. Atrazine degradation capacity of the strain DAT1 and the strain's atrazine-metabolic potential and survival were assessed. The relative abundance of the strain DAT1 and the bacterial community structure in soils were characterized using quantitative PCR in combination with terminal restriction fragment length polymorphism. Atrazine degradation by the strain DAT1 and the strain's atrazine-metabolic potential and survival were not affected by addition of a medium level of nitrate, but these processes were inhibited by addition of a high level of nitrate. Microbial community structure changed in both inoculated and uninoculated microcosms, dependent on the level of added nitrate. Bioaugmentation with the strain DAT1 could be a very efficient biotechnology for bioremediation of soils with high concentrations of atrazine.
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Affiliation(s)
- Xiaode Zhou
- State Key Laboratory of Ecohydraulic Engineering in Shaanxi, Xi'an University of Technology, Xi'an 710048, China
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34
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Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers. Appl Microbiol Biotechnol 2012; 94:851-73. [PMID: 22476263 DOI: 10.1007/s00253-012-4025-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/06/2023]
Abstract
Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
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35
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Wan R, Zhang S, Xie S. Microbial community changes in aquifer sediment microcosm for anaerobic anthracene biodegradation under methanogenic condition. J Environ Sci (China) 2012; 24:1498-1503. [PMID: 23513693 DOI: 10.1016/s1001-0742(11)60959-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The widespread distribution of polycyclic aromatic hydrocarbons (PAHs) in groundwater has become an important environmental issue. Knowledge of microbial community changes could aid in identification of particular microorganisms that are capable of degrading PAHs in contaminated aquifers. Therefore, 16S rRNA gene clone library analysis was used to identify the archaeal and bacterial communities in an aquifer sediment microcosm used for anaerobic anthracene degradation under methanogenic conditions. A remarkable shift of the archaeal community structure occurred after anaerobic anthracene degradation, but the types of the abundant bacterial phyla did not change. However, a decrease of both archaeal and bacterial diversity was observed. Bacterial genera Bacillus, Rhodococcus and Herbaspirillum might have links with anaerobic anthracene degradation, suggesting a role of microbial consortia. This work might add some new information for understanding the mechanism of PAH degradation under methanogenic conditions.
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Affiliation(s)
- Rui Wan
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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