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Zhou J, Feng Y, Wu X, Feng Y, Zhao Y, Pan J, Liu S. Communication leads to bacterial heterogeneous adaptation to changing conditions in partial nitrification reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172110. [PMID: 38565348 DOI: 10.1016/j.scitotenv.2024.172110] [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: 01/24/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Recently, it is reported that bacterial communication coordinates the whole consortia to jointly resist the adverse environments. Here, we found the bacterial communication inevitably distinguished bacterial adaptation among different species in partial nitrification reactor under decreasing temperatures. We operated a partial nitrification reactor under temperature gradient from 30 °C to 5 °C and found the promotion of bacterial communication on adaptation of ammonia-oxidizing bacteria (AOB) was greater than that of nitrite-oxidizing bacteria (NOB). Signal pathways with single-component sensing protein in AOB can regulate more genes involved in bacterial adaptation than that with two-component sensing protein in NOB. The negative effects of bacterial communication, which were seriously ignored, have been highlighted, and Clp regulator downstream diffusible signal factor (DSF) based signal pathways worked as transcription activators and inhibitors of adaptation genes in AOB and NOB respectively. Bacterial communication can induce differential adaptation through influencing bacterial interactions. AOB inclined to cooperate with DSF synthesis bacteria as temperature declined, however, cooperation between NOB and DSF synthesis bacteria inclined to get weakening. According to the regulatory effects of signal pathways, bacterial survival strategies for self-protection were revealed. This study hints a potential way to govern niche differentiation in the microbiota by bacterial communication, contributing to forming an efficient artificial ecosystem.
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Affiliation(s)
- Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Ying Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yunpeng Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Juejun Pan
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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2
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Kaur G, Lecka J, Krol M, Brar SK. Novel BTEX-degrading strains from subsurface soil: Isolation, identification and growth evaluation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122303. [PMID: 37558195 DOI: 10.1016/j.envpol.2023.122303] [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: 05/02/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and o, m, and p-xylenes (BTEX) are high-risk pollutants because of their mutagenic and carcinogenic nature. These pollutants are found with elevated levels in groundwater and soil in Canada at several contaminated sites. The intrinsic microbes present in the subsurface have the potential to degrade pollutants by their metabolic pathways and convert them to non-toxic products. However, the low subsurface temperature (5-10 °C) limits their growth and degradation ability. This study examined the feasibility of subsurface heat augmentation using geothermal heating for BTEX bioremediation. Novel potent BTEX-degrading bacterial strains were isolated from soil at 3.0, 42.6, and 73.2 m depths collected from a geothermal borehole during installation and screened using an enrichment technique. The selected strains were identified with Sanger sequencing and phylogenetic tree analysis, revealing that all the strains except Bacillus subtilis are novel with respective to BTEX degradation. The isolates, Microbacterium esteraromaticum and Bacillus infantis showed the highest degradation with 67.98 and 65.2% for benzene, 72.8 and 71.02% for toluene, 77.52 and 76.44% for ethylbenzene, and 74.58 and 74.04% for xylenes respectively. Further, temperature influence at 15 ± 1 °C, 28 ± 1 °C and 40 ± 1 °C was observed, which showed increased growth by two-fold and on average 35-49% more biodegradation at higher temperatures. Results showed that temperature is a positive stimulant for bioremediation, hence geothermal heating could also be a stimulant for in-situ bioremediation.
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Affiliation(s)
- Gurpreet Kaur
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, M3J 1P3, Canada
| | - Joanna Lecka
- Institut National de La Recherche Scientifique, Centre-Eau, Terre et Environment, 490, Rue de La Couronne, Quebec, G1K 9A9, Canada
| | - Magdalena Krol
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, M3J 1P3, Canada.
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Stanton R, Russell E, Trivedi DJ. Computational Investigations of Metal-Organic Frameworks as Sorbents for BTEX Removal. J Phys Chem Lett 2022; 13:8150-8156. [PMID: 36001471 DOI: 10.1021/acs.jpclett.2c02131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sequestration of aromatic volatile organic compounds (VOCs) via metal-organic frameworks (MOFs) as sorbents is a viable means of environmental preservation. In this investigation, we shed light on the key features associated with MOFs that govern the selective uptake of a subclass of VOCs containing benzene, toluene, ethylbenzene, and xylenes (BTEX). We investigate, through a multistep computational framework including ab initio electronic structure and classical molecular dynamics simulations, the energetic and dynamical properties associated with BTEX capture in three MOFs: HKUST-1, ZIF-8, and MIL-53. Our work demonstrates the importance of considering both static and dynamical properties upon introduction of guest molecules in such computational investigations. We elucidate the key geometric factors associated with efficient capture of BTEX compounds and highlight possible postsynthetic modifications that can be used to produce next generation sorbents for BTEX capture.
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Affiliation(s)
- Robert Stanton
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Emma Russell
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
- Department of Chemical and Biomolecular Engineering, Clarkson University, Potsdam, New York 13699, United States
| | - Dhara J Trivedi
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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4
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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Liu J, Liu Y, Dong W, Li J, Yu S, Wang J, Zuo R. Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics. CHEMOSPHERE 2022; 293:133509. [PMID: 34995620 DOI: 10.1016/j.chemosphere.2021.133509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.
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Affiliation(s)
- Jiayou Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yun Liu
- South China Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, Guangzhou, 510655, China
| | - Weihong Dong
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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Miri S, Rasooli A, Brar SK, Rouissi T, Martel R. Biodegradation of p-xylene-a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21465-21479. [PMID: 34762239 DOI: 10.1007/s11356-021-17387-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 11/02/2021] [Indexed: 05/21/2023]
Abstract
p-Xylene is considered a recalcitrant compound despite showing a similar aromatic structure to other BTEXs (benzene, toluene, ethylbenzene, xylene isomers). This study evaluated the p-xylene biodegradation potential of three psychrophilic Pseudomonas strains (Pseudomonas putida S2TR-01, Pseudomonas synxantha S2TR-20, and Pseudomonas azotoformans S2TR-09). The p-xylene metabolism-related catabolic genes (xylM, xylA, and xylE) and the corresponding regulatory genes (xylR and xylS) of the selected strains were investigated. The biodegradation results showed that the P. azotoformans S2TR-09 strain was the only strain that was able to degrade 200 mg/L p-xylene after 60 h at 15 °C. The gene expression study indicated that the xylE (encoding catechol 2,3-dioxygenase) gene represents the bottleneck in p-xylene biodegradation. A lack of xylE expression leads to the accumulation of intermediates and the inhibition of biomass production and complete carbon recovery. The activity of xylene monooxygenase and catechol 2,3-dioxygenase was significantly increased in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg, respectively) in the presence of p-xylene. The expression of the ring cleavage enzyme and its encoding gene (xylE) and activator (xylS) explained the differences in the p-xylene metabolism of the isolated bacteria and can be used as a novel biomarker of efficient p-xylene biodegradation at contaminated sites.
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Affiliation(s)
- Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Azadeh Rasooli
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada.
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada.
| | - Tarek Rouissi
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Richard Martel
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
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Mahto KU, Kumari S, Das S. Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation. Crit Rev Biochem Mol Biol 2021; 57:305-332. [PMID: 34937434 DOI: 10.1080/10409238.2021.2015747] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.
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Affiliation(s)
- Kumari Uma Mahto
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
| | - Swetambari Kumari
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
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Dangi MB, Urynowicz MA, Schultz CL, Budhathoki S, Dangi SR. Analysis of the effects of in-situ chemical oxidation on microbial activity using Pseudomonas putida F1. Heliyon 2021; 7:e08665. [PMID: 35005293 PMCID: PMC8717238 DOI: 10.1016/j.heliyon.2021.e08665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/03/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022] Open
Abstract
In-situ chemical oxidation is an effective groundwater remediation approach for delivering oxidants to the subsurface environment where various contaminants of concern, natural organic matter, and other reduced species within the soil consume the oxidants. The addition of these oxidants alters microbial activity changing the physical and chemical structure of the soil. This paper studied the effects of chemical oxidation on microbial activity with and without toluene. Several oxidants were used as part of the study: sodium percarbonate, hydrogen peroxide, potassium permanganate, and sodium persulfate evaluated at low, medium, and high concentrations. A series of biometer experiments seeded with microbe Pseudomonas putida F1 and soil sample and aqueous toluene solution for each oxidant was monitored by CO2 production as a function of incubation days to evaluate the effects of oxidation on the microbial activity. Of the oxidants tested, permanganate oxidation resulted in the highest increase in microbial activity post oxidation based on CO2 production both with and without the addition of toluene. The other oxidants exhibited a direct correlation between oxidant concentration and the change in permanganate chemical oxidant demand of the soil. However, there was no correlation between oxidant concentration and microbial activity. Each of the oxidants was shown to increase CO2 yield except for sodium percarbonate, which had an adverse effect on microbial activity. It is likely that the increased microbial activity associated with permanganate oxidation was the result of chemical reactions between the oxidant and natural organic matter in the soil.
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Affiliation(s)
- Mohan B. Dangi
- Department of Geography and City & Regional Planning, California State University, Fresno, CA, 93740, USA
- Corresponding author.
| | - Michael A. Urynowicz
- Department of Civil & Architectural Engineering, University of Wyoming, Laramie, WY, 82071, USA
| | | | - Samir Budhathoki
- Department of Civil & Architectural Engineering, University of Wyoming, Laramie, WY, 82071, USA
| | - Sadikshya R. Dangi
- US Department of Agriculture, Agriculture Research Service, Northern Plains Agricultural Research Laboratory, Sidney, MT, 59270, USA
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Dai Y, Guo Y, Wang J, Li Y, Zhang L, Liu X. A vertically configured photocatalytic-microbial fuel cell for electricity generation and gaseous toluene degradation. CHEMOSPHERE 2021; 285:131530. [PMID: 34273692 DOI: 10.1016/j.chemosphere.2021.131530] [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: 05/10/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
A vertically configured photocatalytic-microbial fuel cell (photo-MFC) is developed by combining a nanodiamond-decorated ZnO (ZnO/ND) photocathode with a bioanode. The system can effectively couple the light energy with bioenergy to enhance the degradation of volatile organic compounds (VOCs) and boost electricity output. Results show that the composite system exhibits increased performance for toluene removal (60.65%), higher than those of individual parts (ZnO/ND-photocatalysis: 37.16%, MFC: 17.81%). Furthermore, its electrochemical performance is dramatically increased. The peak power density of 120 mW/m2 and the current density of 1.07 A/m2 are generated under light illumination, which are about 1.57-fold and 1.37-fold higher than that under dark (76 mW/m2, 0.78 A/m2), respectively. Microbial community analysis demonstrates Proteobacteria and Firmicute are dominant phyla, implying they play important roles on accelerating the extracellular-electron transfer and toluene degradation. In addition, the underlying mechanism for toluene degradation in the photo-MFC system is preliminary explored. Our results suggest that the photo-MFC has great potential for simultaneous treatment of VOCs with energy recovery.
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Affiliation(s)
- Yexin Dai
- Tianjin Key Lab. of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, PR China
| | - Yajing Guo
- Tianjin Key Lab. of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, PR China
| | - Jiao Wang
- Tianjin Key Lab. of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, PR China
| | - Yunxue Li
- Tianjin Key Lab. of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, PR China
| | - Lei Zhang
- School of Life Science, Tianjin University, Tianjin, 300372, PR China
| | - Xianhua Liu
- Tianjin Key Lab. of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, PR China.
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Miri S, Davoodi SM, Karimi Darvanjooghi MH, Brar SK, Rouissi T, Martel R. Precision modelling of co-metabolic biodegradation of recalcitrant aromatic hydrocarbons in conjunction with experimental data. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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