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Yan S, Wang J, Zhang J, Ning J, Chen S, Xie S. Bacterial community composition and function vary with farmland type and soil depth around a mining area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024:124510. [PMID: 39002750 DOI: 10.1016/j.envpol.2024.124510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/04/2024] [Accepted: 07/04/2024] [Indexed: 07/15/2024]
Abstract
Heavy metal pollution can have adverse impacts on microorganisms, plants and even human health. To date, the impact of heavy metals on bacteria in farmland has yielded poor attention, and there is a paucity of knowledge on the impact of land type on bacteria in mining area with heavy metal pollution. Around a metal-contaminated mining area, two soil depths in three types of farmlands were selected to explore the composition and function of bacteria and their correlations with the types and contents of heavy metals. The compositions and functions of bacterial communities at the three different agricultural sites were disparate to a certain extent. Some metabolic functions of bacterial community in the paddy field were up-regulated compared with those at other site. These results observed around mining area were different from those previously reported in conventional farmlands. In addition, bacterial community composition in the top soils was relatively complex, while in the deep soils it became more unitary and extracellular functional genes got enriched. Meanwhile, heavy metal pollution may stimulate the enrichment of certain bacteria to protect plants from damage. This finding may aid in understanding the indirect effect of metal contamination on plants and thus putting forward feasible strategies for the remediation of metal-contaminated sites. MAIN FINDINGS OF THE WORK: This was the first study to comprehensively explore the influence of heavy metal pollution on the soil bacterial communities and metabolic potentials in different agricultural land types and soil depths around a mining area.
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Affiliation(s)
- Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ji Wang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Jianqiang Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Jialian Ning
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, 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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2
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Checa-Fernández A, Santos A, Chicaiza KY, Martin-Sanz JP, Valverde-Asenjo I, Quintana JR, Fernández J, Domínguez CM. Exploring the potential of horse amendment for the remediation of HCHs-polluted soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 364:121436. [PMID: 38875985 DOI: 10.1016/j.jenvman.2024.121436] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024]
Abstract
This study assessed for the first time the bioremediation potential of an organic horse amendment in soils contaminated with solid wastes of the obsolete pesticide lindane (α-hexachlorocyclohexane (α-HCH) = 80 mg kg-1, β-HCH = 40 mg kg-1, γ,δ,ε-HCH≈10 mg kg-1) searching for a self-sufficient bio-based economy. Four treatments were implemented: polluted (PS, ΣHCHs = 130 mg kg-1) and control (CS, ΣHCHs = 1.24 mg kg-1) soils and the respective amended soils (APS and ACS). A commercial amendment, coming from organic wastes, was used for soil biostimulation (5% dry weight), and the temporal evolution of the enzymatic activity (dehydrogenase, β-glucosidase activity, phenoloxidase, arylamidase, phosphatase, and urease) and HCHs concentration of the soils was evaluated over 55 days under controlled humidity and temperature conditions. The horse amendment positively influenced the physicochemical properties of the soil by reducing pH (from 8.3 to 8) and increasing the organic matter (TOC from 0.5 to 3.3%) and nutrient content (P and NH4+ from 24.1 to 13.7 to 142.1 and 41.2 mg kg-1, respectively). Consequently, there was a notable enhancement in the soil biological activity, specifically in the enzymatic activity of dehydrogenase, phenol-oxidase, phosphatase, and urease and, therefore, in HCH degradation, which increased from <1 to 75% after the incubation period. According to the chlorine position on the cyclohexane ring, the following ranking has been found for HCHs degradation: β-HCH (46%) < ε-HCH (57%) < α-HCH (91%) ≈ δ-HCH (91%) < γ-HCH (100%). Pentachlorocyclohexene (PCCH) and 1,2,4-trichlorobenzene (1,2,4-TCB) were identified as HCHs degradation metabolites and disappeared at the end of the incubation time. Although further research is required, these preliminary findings suggest that organic amendments represent a sustainable, harmless, and cost-effective biostimulation approach for remediating soils contaminated with recalcitrant HCHs, boosting the circular economy.
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Affiliation(s)
- Alicia Checa-Fernández
- Department of Chemical Engineering and Materials, Faculty of Chemical Sciences, Complutense University of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Aurora Santos
- Department of Chemical Engineering and Materials, Faculty of Chemical Sciences, Complutense University of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Katherine Yomaira Chicaiza
- Chemical in Pharmaceutical Sciences Department, Faculty of Pharmacy, University Complutense of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Juan P Martin-Sanz
- Chemical in Pharmaceutical Sciences Department, Faculty of Pharmacy, University Complutense of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Inmaculada Valverde-Asenjo
- Chemical in Pharmaceutical Sciences Department, Faculty of Pharmacy, University Complutense of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Jose R Quintana
- Chemical in Pharmaceutical Sciences Department, Faculty of Pharmacy, University Complutense of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Javier Fernández
- Chemical in Pharmaceutical Sciences Department, Faculty of Pharmacy, University Complutense of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain
| | - Carmen M Domínguez
- Department of Chemical Engineering and Materials, Faculty of Chemical Sciences, Complutense University of Madrid, Avenida Complutense s/n, 28040, Madrid, Spain.
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Wang X, Wu Y, Fu C, Zhao W, Li L. Metabolic cross-feeding between the competent degrader Rhodococcus sp. strain p52 and an incompetent partner during catabolism of dibenzofuran: Understanding the leading and supporting roles. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134310. [PMID: 38640677 DOI: 10.1016/j.jhazmat.2024.134310] [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: 02/02/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal.
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Affiliation(s)
- Xudi Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Yanan Wu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Changai Fu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Wenhui Zhao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China.
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Chettri D, Verma AK, Ghosh S, Verma AK. Biogas from lignocellulosic feedstock: current status and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1-26. [PMID: 37697197 DOI: 10.1007/s11356-023-29805-x] [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: 11/06/2022] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
The organic wastes and residues generated from agricultural, industrial, and domestic activities have the potential to be converted to bioenergy. One such energy is biogas, which has already been included in rural areas as an alternative cooking energy source and agricultural activities. It is produced via anaerobic digestion of a wide range of organic nutrient sources and is an essential renewable energy source. The factors influencing biogas yield, i.e., the various substrate, their characteristics, pretreatment methods involved, different microbial types, sources, and inoculum properties, are analyzed. Furthermore, the optimization of these parameters, along with fermentation media optimization, such as optimum pH, temperature, and anaerobic digestion strategies, is discussed. Novel approaches of bioaugmentation, co-digestion, phase separation, co-supplementation, nanotechnology, and biorefinery approach have also been explored for biogas production. Finally, the current challenges and prospects of the process are discussed in the review.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102
| | - Ashwani Kumar Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shilpi Ghosh
- Department of Biotechnology, University of North Bengal, Siliguri, West Bengal, India, 734104
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102.
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Chettri D, Verma AK, Verma AK. Bioaugmentation: an approach to biological treatment of pollutants. Biodegradation 2024; 35:117-135. [PMID: 37684525 DOI: 10.1007/s10532-023-10050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/15/2023] [Indexed: 09/10/2023]
Abstract
Industrial development and the associated generation of waste requires attention for their management, treatment, and reduction without further degrading the quality of life. Microbes and plant-based bioremediation approaches are some of the sustainable strategies for the biodegradation of harmful pollutants instead of chemical-based treatment. Bioaugmentation is one such approach where microbial strains with the ability to degrade the targeted pollutant are introduced in a polluted environment. Harnessing of microbes from various locations, especially from the site of contamination (indigenous microbes), followed by optimization of the strains, inoculum size, media, and genetic engineering of the microbes along with a combination of strategies such as bio stimulation, phytoremediation is being applied to increase the efficiency of bioaugmentation. Further, bioaugmentation is influenced by various factors such as temperature, the composition of the pollutant, and microbial inoculum which needs to be considered for maximum efficiency of the treatment process. It has numerous advantages such as low cost, sustainability, and easy handling of the contaminants however, the major limitation of bioaugmentation is to increase the survival rate of the microbes involved in remediation for a longer duration in such a highly toxic environment. The review discusses these various aspects of bioaugmentation in brief for its large-scale implementation to address the global issue of pollution and environment management.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, 737102, India
| | - Ashwani Kumar Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, 737102, India.
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Masinga P, Simbanegavi TT, Makuvara Z, Marumure J, Chaukura N, Gwenzi W. Emerging organic contaminants in the soil-plant-receptor continuum: transport, fate, health risks, and removal mechanisms. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:367. [PMID: 38488937 DOI: 10.1007/s10661-023-12282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/29/2023] [Indexed: 03/17/2024]
Abstract
There is a lack of comprehensive reviews tracking emerging organic contaminants (EOCs) within the soil-plant continuum using the source-pathway-receptor-impact-mitigation (SPRIM) framework. Therefore, this review examines existing literature to gain insights into the occurrence, behaviour, fate, health hazards, and strategies for mitigating EOCs within the soil-plant system. EOCs identified in the soil-plant system encompass endocrine-disrupting chemicals, surfactants, pharmaceuticals, personal care products, plasticizers, gasoline additives, flame retardants, and per- and poly-fluoroalkyl substances (PFAS). Sources of EOCs in the soil-plant system include the land application of biosolids, wastewater, and solid wastes rich in EOCs. However, less-studied sources encompass plastics and atmospheric deposition. EOCs are transported from their sources to the soil-plant system and other receptors through human activities, wind-driven processes, and hydrological pathways. The behaviour, persistence, and fate of EOCs within the soil-plant system are discussed, including sorption, degradation, phase partitioning, (bio)transformation, biouptake, translocation, and bioaccumulation in plants. Factors governing the behaviour, persistence, and fate of EOCs in the soil-plant system include pH, redox potential, texture, temperature, and soil organic matter content. The review also discusses the environmental receptors of EOCs, including their exchange with other environmental compartments (aquatic and atmospheric), and interactions with soil organisms. The ecological health risks, human exposure via inhalation of particulate matter and consumption of contaminated food, and hazards associated with various EOCs in the soil-plant system are discussed. Various mitigation measures including removal technologies of EOCs in the soil are discussed. Finally, future research directions are presented.
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Affiliation(s)
- Privilege Masinga
- Department of Soil Science and Environment, Faculty of Agriculture, Environment, and Food Systems, University of Zimbabwe, Mount Pleasant, P. O. Box MP 167, Harare, Zimbabwe
| | - Tinoziva T Simbanegavi
- Department of Soil Science and Environment, Faculty of Agriculture, Environment, and Food Systems, University of Zimbabwe, Mount Pleasant, P. O. Box MP 167, Harare, Zimbabwe
| | - Zakio Makuvara
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Jerikias Marumure
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley, 8301, South Africa
| | - Willis Gwenzi
- Biosystems and Engineering Research Group, 380 New Adylin, Marlborough, Harare, Zimbabwe.
- Biosystems and Environmental Engineering Research Group, 380 New Adylin, Marlborough, Harare, Zimbabwe.
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7
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Zhao S, Rogers MJ, Ding C, Xu G, He J. Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4214-4225. [PMID: 38373236 DOI: 10.1021/acs.est.3c09171] [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: 02/21/2024]
Abstract
Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.
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Affiliation(s)
- Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Chang Ding
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research─UFZ, Permoserstraße, 15, Leipzig 04318, Germany
| | - Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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Deka Boruah HP, Chauhan PS, Acharya C. Editorial: Trends of microbial technologies in rehabilitation of contaminated environments. Front Microbiol 2023; 14:1268002. [PMID: 37675427 PMCID: PMC10478085 DOI: 10.3389/fmicb.2023.1268002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
| | - Puneet Singh Chauhan
- Microbial Technologies Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
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Zhang L, Yao G, Mao Z, Song M, Zhao R, Zhang X, Chen C, Zhang H, Liu Y, Wang G, Li F, Wu X. Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131155. [PMID: 36893600 DOI: 10.1016/j.jhazmat.2023.131155] [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: 11/10/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had kcat and Km values of 5.7 s-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.
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Affiliation(s)
- Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaochun Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Chun Chen
- Institute of Biomedicine, Jinan University, Guangzhou, 510632, PR China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
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10
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Wang S, Li S, Du D, Abass OK, Nasir MS, Yan W. Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge. J Environ Sci (China) 2023; 126:742-753. [PMID: 36503799 DOI: 10.1016/j.jes.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/17/2023]
Abstract
The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.
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Affiliation(s)
- Shan Wang
- Department of Environmental Science and Engineering, Xi'an Key Laboratory of Solid Waste Recycling and Resource Recovery, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shanshan Li
- Department of Environmental Science and Engineering, Xi'an Key Laboratory of Solid Waste Recycling and Resource Recovery, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Dan Du
- Department of Environmental Science and Engineering, Xi'an Key Laboratory of Solid Waste Recycling and Resource Recovery, Xi'an Jiaotong University, Xi'an 710049, China
| | - Olusegun K Abass
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Muhammad Salman Nasir
- Department of Environmental Science and Engineering, Xi'an Key Laboratory of Solid Waste Recycling and Resource Recovery, Xi'an Jiaotong University, Xi'an 710049, China; Department of Structures and Environmental Engineering, University of Agriculture, Faisalabad 38040, Pakistan
| | - Wei Yan
- Department of Environmental Science and Engineering, Xi'an Key Laboratory of Solid Waste Recycling and Resource Recovery, Xi'an Jiaotong University, Xi'an 710049, China
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11
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Hirose J. Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation. Microorganisms 2023; 11:microorganisms11020438. [PMID: 36838403 PMCID: PMC9960961 DOI: 10.3390/microorganisms11020438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.
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Affiliation(s)
- Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
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12
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Anand S, Singh A, Kumar V. Recent advancements in cadmium-microbe interactive relations and their application for environmental remediation: a mechanistic overview. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17009-17038. [PMID: 36622611 DOI: 10.1007/s11356-022-25065-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
The toxic and persistent nature of cadmium (Cd) in the environment has become a matter of concern with its drastic increase in the concentrations over past few decades. Among the various techniques, the microbial remediation has been accepted as an effective decontamination tool for environmental applications, which is sustainable over a period of time. The Cd decontamination potential of the microbes depends on various internal and external factors that play a crucial role in selection of the microbes for application in a particular environment. Thus, it is important to understand the role of these factors for optimal application of the microbes. This study provides an insight into the mechanisms involved between the microbes and the environmental Cd. The study also briefly reviews the mathematical models that have been used to predict the remediation potential of the microbes and the kinetics involved during the process. A critical analysis of the recent advancements in the techniques for use of bacteria, fungi, and algal cells to remove Cd has been also presented in the manuscript.
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Affiliation(s)
- Saumya Anand
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004
| | - Ankur Singh
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004
| | - Vipin Kumar
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004.
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13
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Kumar V, Kumar H, Vishal V, Lal S. Studies on the morphology, phylogeny, and bioremediation potential of Penicillium citrinum and Paecilomyces variotii (Eurotiales) from oil-contaminated areas. Arch Microbiol 2023; 205:50. [PMID: 36598589 DOI: 10.1007/s00203-022-03383-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/10/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
Crude oil pollution is one of the most arduous issues to address, as it is hazardous to both public health and the environment. The discovery of novel biosurfactants-producing fungi and bacteria is in high demand due to their excellent properties and wide range of applications. The aim of this research is to isolate a powerful biosurfactant-producing fungus from the crude oil site near Barauni oil refinery in Bihar, India. Standard protocols were used to collect samples from the site. An integrative taxonomic approach was used, which included morphological, molecular, and phylogenetic analysis. The use of plating samples on Bushnell-Hass (BH) media aided in the isolation of a fungal strain from an enrichment culture. Two fungal strains isolated from contaminated soils, Penicillium citrinum and Paecilomyces variotti, showed potent oil degrading activity in a single culture. For preliminary biosurfactants screening, drop collapse assays, oil spreading, and emulsification activity tests were used. The results showed that the cultures performed well in the screening test and were further evaluated for degradation capacity. Different treatment periods (0, 3, 6, 9, 12, and 15 days) were used to observe degradation in single cultures. A steady drop in pH, an alteration in optical density and an increase in carbon dioxide release showed the ability of fungal strain to degrade the crude oil in a single culture. Fungi mycelia provide a larger surface area for absorption and degradation of the pollutants in contaminated environment. They produce extracellular enzymes to degrade the oil, and at the same time absorb and utilise carbon, allowing them to remove toxic substances from the oil. Thus, they could be candidates for bioremediation of a hydrocarbon-contaminated site.
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Affiliation(s)
- Vikas Kumar
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Harsh Kumar
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Vineet Vishal
- Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India.,Department of Botany, Bangabasi Evening College, Kolkata, West Bengal, 700009, India
| | - Shalini Lal
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India. .,Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India.
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14
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Gallego JLR, Peña-Álvarez V, Lara LM, Baragaño D, Forján R, Colina A, Prosenkov A, Peláez AI. Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114267. [PMID: 36368113 DOI: 10.1016/j.ecoenv.2022.114267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.
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Affiliation(s)
- José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain.
| | - Verónica Peña-Álvarez
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain; Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain; University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - Luis M Lara
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain
| | - Diego Baragaño
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain; Department of Environmental Geosciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Czech Republic
| | - Rubén Forján
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain
| | - Arturo Colina
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Mieres, Spain
| | - Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain; University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - Ana Isabel Peláez
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain; University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
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15
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Ke Z, Wang S, Zhu W, Zhang F, Qiao W, Jiang J, Chen K. Genetic bioaugmentation with triclocarban-catabolic plasmid effectively removes triclocarban from wastewater. ENVIRONMENTAL RESEARCH 2022; 214:113921. [PMID: 35863452 DOI: 10.1016/j.envres.2022.113921] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Triclocarban, one of the emerging pollutants, has been accumulating, and it is frequently detected in wastewater. Due to its toxicity and persistence, the efficient removal of triclocarban from wastewater systems is challenging. Genetic bioaugmentation with transferable catabolic plasmids has been considered to be a long-lasting method to clean up pollutants in continuous flow wastewater treatment systems. In this study, bioaugmentation with Pseudomonas putida KT2440, harboring the transferrable triclocarban-catabolic plasmid pDCA-1-gfp-tccA2, rapidly converted 50 μM triclocarban in wastewater into 3,4-dichloroaniline and 4-chloroaniline, which are further mineralized more easily. RT-qPCR results showed that the ratio of the copy number of pDCA-1-gfp-tccA2 to the cell number of strain KT2440 gradually increased during genetic bioaugmentation, suggesting horizontal transfer and proliferation of the plasmid. By using DNA stable isotope probing (SIP) and amplicon sequencing, OTU86 (Escherichia-Shigella), OTU155 (Citrobacter), OTU5 (Brucella), and OTU15 (Enterobacteriaceae) were found to be the potential recipients of the plasmid pDCA-1-gfp-tccA2 in the wastewater bacterial community. Furthermore, three transconjugants in the genera of Escherichia, Citrobacter, and Brucella showing triclocarban-degrading abilities were isolated from the wastewater. This study develops a new method for removing triclocarban from wastewater and provides insights into the environmental behavior of transferrable catabolic plasmids in bacterial community in wastewater systems.
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Affiliation(s)
- Zhuang Ke
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shen Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenqi Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Fu Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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16
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Wang D, Qin L, Liu E, Chai G, Su Z, Shan J, Yang Z, Wang Z, Wang H, Meng H, Zheng X, Li H, Li J, Lin Y. Biodegradation performance and diversity of enriched bacterial consortia capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons. ENVIRONMENTAL TECHNOLOGY 2022; 43:4200-4211. [PMID: 34148513 DOI: 10.1080/09593330.2021.1946163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/13/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are key organic pollutants in the environment that pose threats to the ecosystem and human health. The degradation of high molecular weight (HMW) PAHs by enriched bacterial consortia has been previously studied, while the involved metabolisms and microbial communities are still unclear and warrant further investigations. In this study, five bacterial consortia capable of utilizing different PAHs (naphthalene, anthracene, and pyrene) as the sole carbon and energy sources were enriched from PAH-contaminated soil samples. Among the five consortia, consortium TC exhibited the highest pyrene degradation efficiency (91%) after 19 d of incubation. The degradation efficiency was further enhanced up to 99% by supplementing yeast extract. Besides, consortium TC showed tolerances to high concentrations of pyrene (up to 1000 mg/L) and different heavy metal stresses (including Zn2+, Cd2+, and Pb2+). The dominant genus in consortium TC, GS, and PL showing relatively higher degradation efficiency for anthracene and pyrene was Pseudomonas, whereas consortium PG and GD were predominated by genus Achromobacter and class Enterobacteriaceae, respectively. Consortium TC, as a highly efficient HMW PAH-degrading consortium, could be applied for synergistic biodegradation of HMW PAHs and in situ bioremediation of the sites contaminated with both PAHs and heavy metals.
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Affiliation(s)
- Dongqi Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
- Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, People's Republic of China
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Lu Qin
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Enyu Liu
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Guodong Chai
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Zhenduo Su
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Jiaqi Shan
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Zhangjie Yang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Zhe Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Hui Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Haiyu Meng
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Xing Zheng
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Huaien Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Jiake Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Yishan Lin
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Science, Xi'an, People's Republic of China
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17
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Varner PM, Allemann MN, Michener JK, Gunsch CK. The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation. ENVIRONMENTAL TECHNOLOGY & INNOVATION 2022; 28:102910. [PMID: 37091576 PMCID: PMC10117347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.
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Affiliation(s)
- Paige M. Varner
- Department of Civil and Environmental Engineering, Box 90287, Duke University, Durham, NC 27708, USA
- Corresponding author. (P.M. Varner)
| | - Marco N. Allemann
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Joshua K. Michener
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Claudia K. Gunsch
- Department of Civil and Environmental Engineering, Box 90287, Duke University, Durham, NC 27708, USA
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18
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Kumar M, Bolan N, Jasemizad T, Padhye LP, Sridharan S, Singh L, Bolan S, O'Connor J, Zhao H, Shaheen SM, Song H, Siddique KHM, Wang H, Kirkham MB, Rinklebe J. Mobilization of contaminants: Potential for soil remediation and unintended consequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156373. [PMID: 35649457 DOI: 10.1016/j.scitotenv.2022.156373] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Land treatment has become an essential waste management practice. Therefore, soil becomes a major source of contaminants including organic chemicals and potentially toxic elements (PTEs) which enter the food chain, primarily through leaching to potable water sources, plant uptake, and animal transfer. A range of soil amendments are used to manage the mobility of contaminants and subsequently their bioavailability. Various soil amendments, like desorbing agents, surfactants, and chelating agents, have been applied to increase contaminant mobility and bioavailability. These mobilizing agents are applied to increase the contaminant removal though phytoremediation, bioremediation, and soil washing. However, possible leaching of the mobilized pollutants during soil washing is a major limitation, particularly when there is no active plant uptake. This leads to groundwater contamination and toxicity to plants and soil biota. In this context, the present review provides an overview on various soil amendments used to enhance the bioavailability and mobility of organic and inorganic contaminants, thereby facilitating increased risk when soil is remediated in polluted areas. The unintended consequences of the mobilization methods, when used to remediate polluted sites, are discussed in relation to the leaching of mobilized contaminants when active plant growth is absent. The toxicity of targeted and non-targeted contaminants to microbial communities and higher plants is also discussed. Finally, this review work summarizes the existing research gaps in various contaminant mobilization approaches, and prospects for future research.
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Affiliation(s)
- Manish Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur 440020, Maharashtra, India
| | - Nanthi Bolan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia.
| | - Tahereh Jasemizad
- Department of Civil and Environmental Engineering, Faculty of Engineering, The University of Auckland, Auckland 1010, New Zealand
| | - Lokesh P Padhye
- Department of Civil and Environmental Engineering, Faculty of Engineering, The University of Auckland, Auckland 1010, New Zealand
| | - Srinidhi Sridharan
- CSIR-National Environmental Engineering Research Institute, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Shiv Bolan
- Department of Civil and Environmental Engineering, Faculty of Engineering, The University of Auckland, Auckland 1010, New Zealand
| | - James O'Connor
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Haochen Zhao
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
| | - Sabry M Shaheen
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; King Abdulaziz University, Faculty of Meteorology, Environment, and Arid Land Agriculture, Department of Arid Land Agriculture, 21589 Jeddah, Saudi Arabia
| | - Hocheol Song
- Department of Environment, Energy and Geoinformatics, Sejong University, 98 Gunja-Dong, Guangjin-Gu, Seoul, Republic of Korea
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Hailong Wang
- Biochar Engineering Technology Research Center of Guangdong Province, School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China; Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, Zhejiang A&F University, Hangzhou 311300, China
| | - M B Kirkham
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, United States
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; Department of Environment, Energy and Geoinformatics, Sejong University, 98 Gunja-Dong, Guangjin-Gu, Seoul, Republic of Korea; International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan 173212, Himachal Pradesh, India.
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19
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Deng YD, Wang LJ, Zhang WH, Xu J, Gao JJ, Wang B, Fu XY, Han HJ, Li ZJ, Wang Y, Tian YS, Peng RH, Yao QH. Construction of complete degradation pathway for nitrobenzene in Escherichia coli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:114016. [PMID: 36027713 DOI: 10.1016/j.ecoenv.2022.114016] [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: 03/20/2022] [Revised: 07/31/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Nitrobenzene is widely present in industrial wastewater and soil. Biodegradation has become an ideal method to remediate organic pollutants due to its low cost, high efficiency, and absence of secondary pollution. In the present study, 10 exogenous genes that can completely degrade nitrobenzene were introduced into Escherichia coli, and their successful expression in the strain was verified by fluorescence quantitative polymerase chain reaction and proteomic analysis. The results of the degradation experiment showed that the engineered strain could completely degrade 4 mM nitrobenzene within 8 h. The formation of intermediate metabolites was detected, and the final metabolites entered the E. coli tricarboxylic acid cycle smoothly. This process was discovered by isotope tracing method. Results indicated the integrality of the degradation pathway and the complete degradation of nitrobenzene. Finally, further experiments were conducted in soil to verify its degradation ability and showed that the engineered strain could also degrade 1 mM nitrobenzene within 10 h. In this study, engineered bacteria that can completely degrade nitrobenzene have been constructed successfully. The construction of remediation-engineered bacteria by synthetic biology laid the foundation for the industrial application of biological degradation of organic pollutants.
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Affiliation(s)
- Yong-Dong Deng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Li-Juan Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Wen-Hui Zhang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jing Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jian-Jie Gao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Bo Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiao-Yan Fu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hong-Juan Han
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhen-Jun Li
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yu Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yong-Sheng Tian
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Ri-He Peng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Quan-Hong Yao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
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20
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Eldos HI, Zouari N, Saeed S, Al-Ghouti MA. Recent advances in the treatment of PAHs in the environment: Application of nanomaterial-based technologies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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21
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A Review of Soil Contaminated with Dioxins and Biodegradation Technologies: Current Status and Future Prospects. TOXICS 2022; 10:toxics10060278. [PMID: 35736887 PMCID: PMC9227754 DOI: 10.3390/toxics10060278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022]
Abstract
This article provides a comprehensive assessment of dioxins contaminating the soil and evaluates the bioremediation technology currently being widely used, and also offers recommendations for future prospects. Soil pollution containing dioxins is extremely toxic and hazardous to human health and the environment. Dioxin concentrations in soils around the world are caused by a variety of sources and outcomes, but the main sources are from the consequences of war and human activities. Bioremediation technology (bioaugmentation, biostimulation, and phytoremediation) is considered an optimal and environmentally friendly technology, with the goal of applying native microbial communities and using plant species with a high biomass to treat contaminated dioxins in soil. The powerful bioremediation system is the growth of microorganisms that contribute to the increased mutualistic and competitive relationships between different strains of microorganisms. Although biological treatment technology can thoroughly treat contaminated dioxins in soil with high efficiency, the amount of gas generated and Cl radicals dispersed after the treatment process remains high. Further research on the subject is required to provide stricter control over the outputs noted in this study.
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22
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Hernández-Alomia F, Ballesteros I, Castillejo P. Bioremediation potential of glyphosate-degrading microorganisms in eutrophicated Ecuadorian water bodies. Saudi J Biol Sci 2022; 29:1550-1558. [PMID: 35280549 PMCID: PMC8913404 DOI: 10.1016/j.sjbs.2021.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Phosphonate compounds are the basis of many xenobiotic pollutants, such as Glyphosate (N-(phosphonomethyl-glycine). Only procaryotic microorganisms and the lower eukaryotes are capable of phosphonate biodegradation through C–P lyase pathways. Thus, the aim of this study was to determine the presence of C–P lyase genes in Ecuadorian freshwater systems as a first step towards assessing the presence of putative glyphosate degraders. To that end, two Nested PCR assays were designed to target the gene that codifies for the subunit J (phnJ), which breaks the C-P bond that is critical for glyphosate mineralization. The assays designed in this study led to the detection of phnJ genes in 7 out of 8 tested water bodies. The amplified fragments presented 85–100% sequence similarity with phnJ genes that belong to glyphosate-degrading microorganisms. Nine sequences were not reported previously in the GenBank. The presence of phosphonate degraders was confirmed by isolating three strains able to grow using glyphosate as a unique carbon source. According to the 16S sequence, these strains belong to the Pantoea, Pseudomonas, and Klebsiella genera. Performing a Nested PCR amplification of phnJ genes isolated from eutrophicated water bodies, prior to isolation, may be a cost-effective strategy for the bioprospection of new species and/or genes that might have new properties for biotech industries, laying the groundwork for additional research.
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Affiliation(s)
- Fernanda Hernández-Alomia
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Isabel Ballesteros
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
- Corresponding author.
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Szentgyörgyi F, Benedek T, Fekete D, Táncsics A, Harkai P, Kriszt B. Development of a bacterial consortium from Variovorax paradoxus and Pseudomonas veronii isolates applicable in the removal of BTEX. AMB Express 2022; 12:4. [PMID: 35075552 PMCID: PMC8787013 DOI: 10.1186/s13568-022-01349-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/16/2022] [Indexed: 12/07/2022] Open
Abstract
In this study, we report on the development of a novel bacterial consortium, consisting of Variovorax paradoxus and Pseudomonas veronii isolates, applicable in the biodegradation of all six BTEX compounds (benzene, toluene, ethylbenzene, o-, m- and p-xylene) and the bioremediation of contaminated sites. The co-cultivability of the selected bacterial isolates was determined in nutrient-rich medium, as well as in BTEX amended mineral salts solution using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and CFU determinations. BTEX biodegradation capacity of the two-strain consortium was assessed in mineral salts solution, where a series of BTEX depletions and supplementations occurred, as well as in a real, BTEX polluted environmental sample (contaminated groundwater) in the presence of the autochthonous bacterial community. The obtained results indicated that the developed bacterial consortium is very efficient in BTEX biodegradation. Under laboratory conditions, the acclimatized bacterial consortium completely degraded the BTEX mixture with a concentration as high as 20 mg l-1 in a mineral salt medium within a short span of 6 h. Close to in situ groundwater conditions (incubated at 15 °C under static conditions in the absence of light), groundwater microcosms containing the autochthonous bacterial community inoculated with the developed bacterial consortium showed more efficient toluene, o-, m-and p-xylene biodegradation capacity than microcosms containing solely the native microbial population originally found in the groundwater. In the inoculated microcosms, after 115 h of incubation the concentration (~ 1.7 mg l-1 each) of o-, m- and p-xylene decreased to zero, whereas in the non-inoculated microcosms the concentration of xylene isomers was still 0.2, 0.3 and 0.3 mg l-1, respectively. The allochthonous bioaugmentation of the contaminated groundwater with the obtained inoculant was successful and manifested in a better BTEX degradation rate. Our results suggest that the obtained bacterial consortium can be a new, stable and efficient bioremediation agent applicable in the synergistic elimination of BTEX compounds from contaminated sites.
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Hall JPJ, Harrison E, Baltrus DA. Introduction: the secret lives of microbial mobile genetic elements. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200460. [PMID: 34839706 PMCID: PMC8628069 DOI: 10.1098/rstb.2020.0460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
| | - David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721‐0036, USA
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25
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Zhao G, Wu Y, Wang X, Chen M, Li L. The impact of pollutant as selection pressure on conjugative transfer of dioxin-catabolic plasmids harbored by Rhodococcus sp. strain p52. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1470-1481. [PMID: 34355316 DOI: 10.1007/s11356-021-15682-9] [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: 03/17/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Plasmid-mediated bioaugmentation has potential application in the cleanup of recalcitrant environmental pollutants. In this study, we examined the influence of various contaminants (in different categories or different amounts) as a selection pressure on the spread of catabolic plasmids within an activated sludge bacteria community bioaugmented with Rhodococcus sp. strain p52 harboring pDF01 and pDF02. The distinguishable genera of transconjugants were isolated under the stresses of phenanthrene, dibenzothiophene, and dibenzo-p-dioxin. The three contaminants exerted different degrees of influence on the activated sludge bacteria bearing the catabolic plasmids. The relatively high ratios of transconjugant-bearing catabolic plasmids were detected in the reactor fed with dibenzo-p-dioxin. As dibenzo-p-dioxin from 10 to 80 mg/L was fed into the reactors, the ratios of transconjugant-bearing catabolic plasmids increased. Additionally, levels of ROS and extracellular LDH of activated sludge bacteria in the contaminants-fed reactors increased, comparing with that in the control reactor, indicating that the contaminants exerted toxicity which promoted the cell membrane permeability of the activated sludge bacteria. Our study provides a characterization of the recalcitrant contaminants as a selection pressure that can modulate catabolic plasmid transfer during genetic bioaugmentation for the removal of contaminants.
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Affiliation(s)
- Gang Zhao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 72 Binhai Road, Jimo, 266237, China
| | - Yanan Wu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 72 Binhai Road, Jimo, 266237, China
| | - Xu Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 72 Binhai Road, Jimo, 266237, China
| | - Meng Chen
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 72 Binhai Road, Jimo, 266237, China
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 72 Binhai Road, Jimo, 266237, China.
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Abstract
Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, but their bioremediation capabilities vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Plasmids are extrachromosomal DNA elements that can often transfer between bacteria and facilitate the flow of genetic information across microbiomes, yet their ability to spread within rapid sand filters has remained unknown. Here, we examine the permissiveness of rapid sand filter communities toward four environmentally transmissible plasmids, RP4, RSF1010, pKJK5, and TOL (pWWO), using a dual-fluorescence bioreporter platform combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their potential suitability for introducing bioremediation determinants in the microbiomes of underperforming water purification plants.
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Mawang CI, Azman AS, Fuad ASM, Ahamad M. Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00679. [PMID: 34660214 PMCID: PMC8503819 DOI: 10.1016/j.btre.2021.e00679] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 08/05/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
Abstract
Over the past two decades, various eco-friendly approaches utilizing microbial species to clean up contaminated environments have surfaced. In this aspect, actinobacteria have demonstrated their potential in contaminant degradation. The members of actinobacteria phylum exhibits a cosmopolitan distribution, which means that they can be found widely in both aquatic and terrestrial ecosystems. Actinobacteria play important ecological roles in the environment, such as degrading complex polymers, recycling compounds, and producing bioactive molecules. Hence, using actinobacteria to clean up contaminants is an attractive method in the field of biotechnology. This can be achieved through the green technology of bioaugmentation, whereby the degradative capacity of contaminated areas can be greatly improved through the introduction of specific microorganisms. This review describes actinobacteria as an eco-friendly and a promising technology for the bioaugmentation of contaminants, with focus on pesticides and heavy metals.
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Affiliation(s)
- Christina-Injan Mawang
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Setia Alam, Shah Alam, Selangor, 40170, Malaysia
| | - Adzzie-Shazleen Azman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, 47500, Malaysia
| | - Aalina-Sakiinah Mohd Fuad
- Department of Biomedical Science, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia Kuantan Campus, Jalan Sultan Ahmad Shah, Bandar Indera Mahkota, Kuantan, Pahang 25200, Malaysia
| | - Mariana Ahamad
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Setia Alam, Shah Alam, Selangor, 40170, Malaysia
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28
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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29
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Wang B, Gao J, Xu J, Fu X, Han H, Li Z, Wang L, Zhang F, Tian Y, Peng R, Yao Q. Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126428. [PMID: 34171665 DOI: 10.1016/j.jhazmat.2021.126428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a 13C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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30
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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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Li J, Jia C, Lu Q, Hungate BA, Dijkstra P, Wang S, Wu C, Chen S, Li D, Shim H. Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126384. [PMID: 34329005 DOI: 10.1016/j.jhazmat.2021.126384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.
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Affiliation(s)
- Junhui Li
- Vanderbilt Microbiome Initiative, Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.
| | - Chongjian Jia
- Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Cuiyu Wu
- College of Natural Resources and Environmental Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Deqiang Li
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR 999078, China.
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32
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Dell’ Anno F, Rastelli E, Sansone C, Brunet C, Ianora A, Dell’ Anno A. Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era. Microorganisms 2021; 9:1695. [PMID: 34442774 PMCID: PMC8400010 DOI: 10.3390/microorganisms9081695] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022] Open
Abstract
Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.
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Affiliation(s)
- Filippo Dell’ Anno
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Antonio Dell’ Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Cyriaque V, Madsen JS, Fievez L, Leroy B, Hansen LH, Bureau F, Sørensen SJ, Wattiez R. Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community. Front Microbiol 2021; 12:655903. [PMID: 34122370 PMCID: PMC8195591 DOI: 10.3389/fmicb.2021.655903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.
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Affiliation(s)
- Valentine Cyriaque
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium.,Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laurence Fievez
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Lars H Hansen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabrice Bureau
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
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Properties affecting transfer and expression of degradative plasmids for the purpose of bioremediation. Biodegradation 2021; 32:361-375. [PMID: 34046775 DOI: 10.1007/s10532-021-09950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/15/2021] [Indexed: 10/21/2022]
Abstract
Plasmids, circular DNA that exist and replicate outside of the host chromosome, have been important in the spread of non-essential genes as well as the rapid evolution of prokaryotes. Recent advances in environmental engineering have aimed to utilize the mobility of plasmids carrying degradative genes to disseminate them into the environment for cost-effective and environmentally friendly remediation of harmful contaminants. Here, we review the knowledge surrounding plasmid transfer and the conditions needed for successful transfer and expression of degradative plasmids. Both abiotic and biotic factors have a great impact on the success of degradative plasmid transfer and expression of the degradative genes of interest. Properties such as ecological growth strategies of bacteria may also contribute to plasmid transfer and may be an important consideration for bioremediation applications. Finally, the methods for detection of conjugation events have greatly improved and the application of these tools can help improve our understanding of conjugation in complex communities. However, it remains clear that more methods for in situ detection of plasmid transfer are needed to help detangle the complexities of conjugation in natural environments to better promote a framework for precision bioremediation.
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Bhatt P, Gangola S, Bhandari G, Zhang W, Maithani D, Mishra S, Chen S. New insights into the degradation of synthetic pollutants in contaminated environments. CHEMOSPHERE 2021; 268:128827. [PMID: 33162154 DOI: 10.1016/j.chemosphere.2020.128827] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/28/2020] [Indexed: 05/11/2023]
Abstract
The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Geeta Bhandari
- Department of Biotechnology, Sardar Bhagwan Singh University, Dehradun, 248161, Uttarakhand, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology, Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
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Liu Y, Zhang H, He X, Liu J. Genetically Engineered Methanotroph as a Platform for Bioaugmentation of Chemical Pesticide Contaminated Soil. ACS Synth Biol 2021; 10:487-494. [PMID: 33616380 DOI: 10.1021/acssynbio.0c00532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioaugmentation is a promising alternative in soil remediation. One challenge of bioaugmentation is that exogenous pollutant-degrading microbes added to soil cannot establish enough biomass to eliminate pollutants. Considering that methanotrophs have a growth advantage in the presence of methane, we hypothesize that genetically engineered methanotrophs could degrade contaminants efficiently in soil with methane. Here, methanotroph Methylomonas sp. LW13, herbicide bensulfuron-methyl (BSM), and two kinds of soil were chosen to confirm this hypothesis. The unmarked gene knock-in method was first developed for strain LW13. Then, BSM hydrolase encoding gene sulE was inserted into the chromosome of strain LW13, conferring it BSM-degrading ability. After inoculation, the cell amount of strain LW13-sulE in soil raised considerably (over 100 fold in 9 days) with methane provision; meanwhile, >90% of BSM in soil was degraded. This study provides a proof of the concept that genetically engineered methanotroph is a potential platform for soil remediation.
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Affiliation(s)
- Yongchuang Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Haili Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Xiangrong He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China
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Galitskaya P, Biktasheva L, Kuryntseva P, Selivanovskaya S. Response of soil bacterial communities to high petroleum content in the absence of remediation procedures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:9610-9627. [PMID: 33155112 DOI: 10.1007/s11356-020-11290-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.
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Affiliation(s)
- Polina Galitskaya
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008
| | - Liliya Biktasheva
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008.
| | - Polina Kuryntseva
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008
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Bravo G, Vega-Celedón P, Gentina JC, Seeger M. Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms. Microorganisms 2020; 8:E1952. [PMID: 33316980 PMCID: PMC7763483 DOI: 10.3390/microorganisms8121952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20-30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities.
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Affiliation(s)
- Guillermo Bravo
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
| | - Paulina Vega-Celedón
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
| | - Juan Carlos Gentina
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso 2362803, Chile;
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
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Garbisu C, Alkorta I, Kidd P, Epelde L, Mench M. Keep and promote biodiversity at polluted sites under phytomanagement. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44820-44834. [PMID: 32975751 DOI: 10.1007/s11356-020-10854-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.
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Affiliation(s)
- Carlos Garbisu
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia P812, E-48160, Derio, Spain.
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P. O. Box 644, 48080, Bilbao, Spain
| | - Petra Kidd
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Investigacións Agrobiolóxicas de Galicia (IIAG), 15780, Santiago de Compostela, Spain
| | - Lur Epelde
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia P812, E-48160, Derio, Spain
| | - Michel Mench
- INRAE, BIOGECO, University of Bordeaux, F-33615, Pessac, France
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Carraro N, Sentchilo V, Polák L, Bertelli C, van der Meer JR. Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1. Genes (Basel) 2020; 11:genes11080930. [PMID: 32806781 PMCID: PMC7466150 DOI: 10.3390/genes11080930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1's chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). P. nitroreducens carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICEclc of Pseudomonas knackmussii B13. The variable regions of ICEPni1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICEPni2 (171 kb) encodes complete meta-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10-6-10-8 per P. nitroreducens HBP-1 donor into Pseudomonas putida, where they integrated site specifically into tRNAGly-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.
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Affiliation(s)
- Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
- Correspondence:
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
| | - Lenka Polák
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
| | - Claire Bertelli
- Institute for Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland;
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
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41
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Purohit J, Chattopadhyay A, Teli B. Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application. Curr Genomics 2020; 21:253-270. [PMID: 33071619 PMCID: PMC7521044 DOI: 10.2174/1389202921999200525155711] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Since the last few decades, the promiscuous and uncontrolled use of plastics led to the accumulation of millions of tons of plastic waste in the terrestrial and marine environment. It elevated the risk of environmental pollution and climate change. The concern arises more due to the reckless and unscientific disposal of plastics containing high molecular weight polymers, viz., polystyrene, polyamide, polyvinylchloride, polypropylene, polyurethane, and polyethylene, etc. which are very difficult to degrade. Thus, the focus is now paid to search for efficient, eco-friendly, low-cost waste management technology. Of them, degradation of non-degradable synthetic polymer using diverse microbial agents, viz., bacteria, fungi, and other extremophiles become an emerging option. So far, very few microbial agents and their secreted enzymes have been identified and characterized for plastic degradation, but with low efficiency. It might be due to the predominance of uncultured microbial species, which consequently remain unexplored from the respective plastic degrading milieu. To overcome this problem, metagenomic analysis of microbial population engaged in the plastic biodegradation is advisable to decipher the microbial community structure and to predict their biodegradation potential in situ. Advancements in sequencing technologies and bioinformatics analysis allow the rapid metagenome screening that helps in the identification of total microbial community and also opens up the scope for mining genes or enzymes (hydrolases, laccase, etc.) engaged in polymer degradation. Further, the extraction of the core microbial population and their adaptation, fitness, and survivability can also be deciphered through comparative metagenomic study. It will help to engineer the microbial community and their metabolic activity to speed up the degradation process.
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Affiliation(s)
- Jyotika Purohit
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
| | - Anirudha Chattopadhyay
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
| | - Basavaraj Teli
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
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Hall JPJ, Harrison E, Pärnänen K, Virta M, Brockhurst MA. The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer. Front Microbiol 2020; 11:1846. [PMID: 32849443 PMCID: PMC7419628 DOI: 10.3389/fmicb.2020.01846] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Carriage of resistance genes can underpin bacterial survival, and by spreading these genes between species, mobile genetic elements (MGEs) can potentially protect diversity within microbial communities. The spread of MGEs could be affected by environmental factors such as selection for resistance, and biological factors such as plasmid host range, with consequences for individual species and for community structure. Here we cultured a focal bacterial strain, Pseudomonas fluorescens SBW25, embedded within a soil microbial community, with and without mercury selection, and with and without mercury resistance plasmids (pQBR57 or pQBR103), to investigate the effects of selection and resistance gene introduction on (1) the focal species; (2) the community as a whole; (3) the spread of the introduced mer resistance operon. We found that P. fluorescens SBW25 only escaped competitive exclusion by other members of community under mercury selection, even when it did not begin with a mercury resistance plasmid, due to its propensity to acquire resistance from the community by horizontal gene transfer. Mercury pollution had a significant effect on community structure, decreasing alpha diversity within communities while increasing beta diversity between communities, a pattern that was not affected by the introduction of mercury resistance plasmids by P. fluorescens SBW25. Nevertheless, the introduced merA gene spread to a phylogenetically diverse set of recipients over the 5 weeks of the experiment, as assessed by epicPCR. Our data demonstrates how the effects of MGEs can be experimentally assessed for individual lineages, the wider community, and for the spread of adaptive traits.
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Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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Tumolo M, Ancona V, De Paola D, Losacco D, Campanale C, Massarelli C, Uricchio VF. Chromium Pollution in European Water, Sources, Health Risk, and Remediation Strategies: An Overview. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E5438. [PMID: 32731582 PMCID: PMC7432837 DOI: 10.3390/ijerph17155438] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 01/23/2023]
Abstract
Chromium is a potentially toxic metal occurring in water and groundwater as a result of natural and anthropogenic sources. Microbial interaction with mafic and ultramafic rocks together with geogenic processes release Cr (VI) in natural environment by chromite oxidation. Moreover, Cr (VI) pollution is largely related to several Cr (VI) industrial applications in the field of energy production, manufacturing of metals and chemicals, and subsequent waste and wastewater management. Chromium discharge in European Union (EU) waters is subjected to nationwide recommendations, which vary depending on the type of industry and receiving water body. Once in water, chromium mainly occurs in two oxidation states Cr (III) and Cr (VI) and related ion forms depending on pH values, redox potential, and presence of natural reducing agents. Public concerns with chromium are primarily related to hexavalent compounds owing to their toxic effects on humans, animals, plants, and microorganisms. Risks for human health range from skin irritation to DNA damages and cancer development, depending on dose, exposure level, and duration. Remediation strategies commonly used for Cr (VI) removal include physico-chemical and biological methods. This work critically presents their advantages and disadvantages, suggesting a site-specific and accurate evaluation for choosing the best available recovering technology.
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Affiliation(s)
- Marina Tumolo
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
- Department of Biology, University of Bari, 70126 Bari, Italy
| | - Valeria Ancona
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, Italian National Research Council (IBBR-CNR), 70126 Bari, Italy;
| | - Daniela Losacco
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
- Department of Biology, University of Bari, 70126 Bari, Italy
| | - Claudia Campanale
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
| | - Carmine Massarelli
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
| | - Vito Felice Uricchio
- Water Research, Institute-Italian National Research Council (IRSA-CNR), 70132 Bari, Italy; (M.T.); (D.L.); (C.C.); (C.M.); (V.F.U.)
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Liang B, Yun H, Kong D, Ding Y, Li X, Vangnai AS, Wang A. Bioaugmentation of triclocarban and its dechlorinated congeners contaminated soil with functional degraders and the bacterial community response. ENVIRONMENTAL RESEARCH 2020; 180:108840. [PMID: 31654905 DOI: 10.1016/j.envres.2019.108840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Partial removal of haloaromatic antimicrobial triclocarban (TCC) during wastewater treatment caused the final introduction of residual TCC into soils. Bioaugmentation has been proposed for the biodegradation of TCC and its dechlorinated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) in soil. The isolated TCC-degrading strain Ochrobactrum sp. TCC-2 and chloroanilines-degrading strain Diaphorobacter sp. LD72 were used to study the removal efficiency of TCC, DCC and NCC mixture and their chloroanilines intermediates, respectively. The potential degradation competition between TCC and its dechlorinated congeners, and the response of bacterial community during the bioremediation were also investigated. The biodegradation of DCC and TCC was significantly enhanced for soil with inoculums compared with sterilized and natural soils. Chloroanilines products could also be effectively removed. For the degradation of combined substrates in the aqueous medium, NCC had negative effect on the degradation of TCC and DCC, while TCC and DCC negatively influenced each other. The bioaugmentation with two degraders obviously changed the phylogenetic composition and function of indigenous soil microbiome. Importantly, the inoculated degraders could be maintained, suggesting their adaptability and potential application in bioaugmentation for such recalcitrant contaminants. This study offers new insights into the enhanced bioremediation of TCC and its dechlorinated congeners contaminated soils by the bioaugmentation of functional degraders and the structure and function response of the indigenous soil microbiome to the bioremediation process.
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Affiliation(s)
- Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui Yun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Deyong Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Shenyang Academy of Environmental Sciences, Shenyang, 110167, China
| | - Yangcheng Ding
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China
| | - Alisa S Vangnai
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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Conjugative transfer of Megaplasmids pND6–1 and pND6–2 enhancing naphthalene degradation in aqueous environment: characterization and bioaugmentation prospects. Appl Microbiol Biotechnol 2019; 104:861-871. [DOI: 10.1007/s00253-019-10273-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/27/2022]
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Sysoeva TA, Kim Y, Rodriguez J, Lopatkin AJ, You L. Growth‐stage‐dependent regulation of conjugation. AIChE J 2019. [DOI: 10.1002/aic.16848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Tatyana A. Sysoeva
- Department of Biomedical EngineeringDuke University Durham North Carolina
- Department of Biological SciencesThe University of Alabama in Huntsville Huntsville Alabama
| | - Youlim Kim
- Department of Biomedical EngineeringDuke University Durham North Carolina
| | - Jonathan Rodriguez
- Department of Biomedical EngineeringDuke University Durham North Carolina
| | | | - Lingchong You
- Department of Biomedical EngineeringDuke University Durham North Carolina
- Center for Genomic and Computational BiologyDuke University Durham North Carolina
- Department of Molecular Genetics and MicrobiologyDuke University School of Medicine North Carolina
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Remediation of Organically Contaminated Soil Through the Combination of Assisted Phytoremediation and Bioaugmentation. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9224757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Here, we aimed to bioremediate organically contaminated soil with Brassica napus and a bacterial consortium. The bioaugmentation consortium consisted of four endophyte strains that showed plant growth-promoting traits (three Pseudomonas and one Microbacterium) plus three strains with the capacity to degrade organic compounds (Burkholderia xenovorans LB400, Paenibacillus sp. and Lysinibacillus sp.). The organically contaminated soil was supplemented with rhamnolipid biosurfactant and sodium dodecyl benzenesulfonate to increase the degradability of the sorbed contaminants. Soils were treated with organic amendments (composted horse manure vs. dried cow slurry) to promote plant growth and stimulate soil microbial activity. Apart from quantification of the expected decrease in contaminant concentrations (total petroleum hydrocarbons, polycyclic aromatic hydrocarbons), the effectiveness of our approach was assessed in terms of the recovery of soil health, as reflected by the values of different microbial indicators of soil health. Although the applied treatments did not achieve a significant decrease in contaminant concentrations, a significant improvement of soil health was observed in our amended soils (especially in soils amended with dried cow slurry), pointing out a not-so-uncommon situation in which remediation efforts fail from the point of view of the reduction in contaminant concentrations while succeeding to recover soil health.
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Nanda M, Kumar V, Sharma DK. Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to 'clean-up' heavy metal contaminants from water. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 212:1-10. [PMID: 31022608 DOI: 10.1016/j.aquatox.2019.04.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 05/27/2023]
Abstract
Heavy metal pollution is one of the major environmental concerns worldwide. Toxic heavy metals when untreated get accumulated in environment and can pose severe threats to living organisms. It is well known that metals play a major role either directly or indirectly in different metabolic processes of bacteria. This allows bacterial cells to grow even in the presence of some toxic heavy metals. Microbial biotechnology has thus emerged as an effective and eco friendly solution in recent years for bioremediation of heavy metals. Therefore, this review is focused on summarising bacterial adaptation mechanisms for various heavy metals. It also shares some applications of have metal tolerant bacteria in bioremediation. Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation strategies. The genetic determinants for most of these resistances are located on plasmids however some may be chromosomal as well. Bacterial cells can uptake heavy by both ATP dependent and ATP independent processes. Bacterial cell wall also plays a very important role in accumulating heavy metals by bacterial cells. Gram-positive bacteria accumulate much higher concentrations of heavy metals on their cell walls than that of metals gram -ve bacteria. The role of bacterial metallothioneins (MTs) in heavy metal has also been reported. Thus, heavy metal tolerant bacteria are important for bioremediation of heavy metal pollutants from areas containing high concentrations of particular heavy metals.
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Affiliation(s)
- Manisha Nanda
- Department of Biotechnology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Dehradun, 248007, India.
| | - Vinod Kumar
- Department of Chemistry, Uttaranchal University, Dehradun, 248007, India.
| | - D K Sharma
- Department of Zoology and Biotechnology, H.N.B. Garhwal Central University, SRT Campus, Badshahi Thaul, Tehri, Uttarakhand, India
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Jung CM, Carr M, Blakeney GA, Indest KJ. Enhanced plasmid-mediated bioaugmentation of RDX-contaminated matrices in column studies using donor strain Gordonia sp. KTR9. J Ind Microbiol Biotechnol 2019; 46:1273-1281. [PMID: 31119503 DOI: 10.1007/s10295-019-02185-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/29/2019] [Indexed: 11/30/2022]
Abstract
Horizontal gene transfer (HGT) is the lateral movement of genetic material between organisms. The RDX explosive-degrading bacterium Gordonia sp. KTR9 has been shown previously to transfer the pGKT2 plasmid containing the RDX degradative genes (xplAB) by HGT. Overall, fitness costs to the transconjugants to maintain pGKT2 was determined through growth and survivability assessments. Rhodococcus jostii RHA1 transconjugants demonstrated a fitness cost while other strains showed minimal cost. Biogeochemical parameters that stimulate HGT of pGKT2 were evaluated in soil slurry mating experiments and the absence of nitrogen was found to increase HGT events three orders of magnitude. Experiments evaluating RDX degradation in flow-through soil columns containing mating pairs showed 20% greater degradation than columns with only the donor KTR9 strain. Understanding the factors governing HGT will benefit bioaugmentation efforts where beneficial bacteria with transferrable traits could be used to more efficiently degrade contaminants through gene transfer to native populations.
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Affiliation(s)
- Carina M Jung
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA.
| | - Matthew Carr
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
| | - G Alon Blakeney
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
| | - Karl J Indest
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA.
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Madrid F, Rubio-Bellido M, Villaverde J, Peña A, Morillo E. Natural and assisted dissipation of polycyclic aromatic hydrocarbons in a long-term co-contaminated soil with creosote and potentially toxic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:705-714. [PMID: 30743956 DOI: 10.1016/j.scitotenv.2018.12.376] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/10/2018] [Accepted: 12/24/2018] [Indexed: 05/20/2023]
Abstract
An enhanced bioremediation strategy was applied to an industrial soil co-contaminated with Polycyclic Aromatic Hydrocarbons (PAHs) and Potentially Toxic Elements (PTEs). Hydroxypropyl-β-cyclodextrin (HPBCD) and a natural mixture of two rhamnolipids (RL) were added to increase PAHs bioavailability, and combined with a microbial consortium (MC) to biodegrade soil PAHs. Bioavailability of only six PAHs (3-, 4-ring PAHs) increased when using HPBCD, with a maximum increase about 2.8-fold higher. The highest dose of HPBCD (5%) enhanced PAH degradation, with the best results for 4-ring PAHs with treatments of HPBCD + MC (up to 48% degradation for pyrene and 43% for fluoranthene), whereas dissipation for 5-ring PAHs was very low and for 6-ring was negligible. The use of RL increased the bioavailability of 13 of the 16 PAHs studied, reaching up to 60-fold higher values for phenanthrene or 18-fold higher for acenaphtene. RL addition did not show degradation improvement in any situation, and even inhibited the scarce degradation observed in the control treatment. The high increase in availability of both PAHs and mainly PTEs when using RL as amendment could make them toxic for microorganisms. In fact, Microtox Acute Toxicity test using Aliivibrio fischeri and the absence of colony forming units (CFUs) of indigenous bacteria demonstrated the extremely high levels of toxicity in RL treated soil.
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Affiliation(s)
- F Madrid
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Sevilla, Spain
| | - M Rubio-Bellido
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Sevilla, Spain
| | - J Villaverde
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Sevilla, Spain
| | - A Peña
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Avda. de las Palmeras 4, 18100, Armilla, Granada, Spain
| | - E Morillo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Sevilla, Spain.
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