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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [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: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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2
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [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: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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3
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Ivy N, Mukherjee T, Bhattacharya S, Ghosh A, Sharma P. Arsenic contamination in groundwater and food chain with mitigation options in Bengal delta with special reference to Bangladesh. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:1261-1287. [PMID: 35841495 DOI: 10.1007/s10653-022-01330-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Bangladesh, situated in Bengal delta, is one of the worst affected countries by arsenic contamination in groundwater. Most of the people in the country are dependent on groundwater for domestic and irrigation purposes. Currently, 61 districts out of 64 districts of Bangladesh are affected by arsenic contamination. Drinking arsenic contaminated groundwater is the main pathway of arsenic exposure in the population. Additionally, the use of arsenic-contaminated groundwater for irrigation purpose in crop fields in Bangladesh has elevated arsenic concentration in surface soil and in the plants. In many arsenic-affected countries, including Bangladesh, rice is reported to be one of the significant sources of arsenic contamination. This review discussed scenario of groundwater arsenic contamination and transmission of arsenic through food chain in Bangladesh. The study further highlighted the human health perspectives of arsenic exposure in Bangladesh with possible mitigation and remediation options employed in the country.
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Affiliation(s)
- Nishita Ivy
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar, India
| | | | - Sayan Bhattacharya
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar, India
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Prabhakar Sharma
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar, India.
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Cai X, Xue C, Owens G, Chen Z. Removal of As(III) using a microorganism sustained secrete laccase-straw oxidation system. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130967. [PMID: 36764251 DOI: 10.1016/j.jhazmat.2023.130967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
While laccase oxidation is a novel and promising method for treating arsenite-containing wastewater, the high cost and unsustainability of commercially available enzymes indicate a need to investigate more cost-effective viable alternatives. Here, a microorganism sustained secrete laccase-straw oxidation system (MLOS) was established and subsequently evaluated for the removal of As(III). MLOS showed efficient biological As(III) oxidation, with an As(III) removal efficiency reaching 99.9% at an initial As(III) concentration of 1.0 mg·L-1. IC-AFS and XPS analysis showed that As(III) was partially oxidized to As(V), and partially As(III) adsorbed on the surface of rice straw. FTIR analysis revealed that hydroxyl, amine and amide groups were all involved in the As(III) removal process. SEM-EDS demonstrated that the surface structure of rice straw was destroyed following Comamonas testosteroni FJ17 (C. testosteroni FJ17) treatment, and the metal ions binding sites of rice straw were increased resulting in elemental arsenic being detected on the material surface. Molecular docking revealed the interaction between key residues of laccase and As(III). Laccase activity was negatively correlated with Cu(II) concentration in the As(III) oxidation. EEM showed that humic-like acids were also involved in the interaction with As(III). Overall, a MLOS derived from biomass waste has a significant potential to be developed as a green and sustainable technology for the treatment of wastewater containing As(III).
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Affiliation(s)
- Xiaonan Cai
- College of Environmental and Resource Sciences, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China
| | - Chao Xue
- College of Environmental and Resource Sciences, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China.
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australian, Mawson Lakes, SA 5095, Australia
| | - Zuliang Chen
- College of Environmental and Resource Sciences, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China.
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5
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Biotechnology Advances in Bioremediation of Arsenic: A Review. Molecules 2023; 28:molecules28031474. [PMID: 36771138 PMCID: PMC9921067 DOI: 10.3390/molecules28031474] [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: 12/26/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Arsenic is a highly toxic metalloid widespread in the Earth's crust, and its contamination due to different anthropogenic activities (application of agrochemicals, mining, waste management) represents an emerging environmental issue. Therefore, different sustainable and effective remediation methods and approaches are needed to prevent and protect humans and other organisms from detrimental arsenic exposure. Among numerous arsenic remediation methods, those supported by using microbes as sorbents (microbial remediation), and/or plants as green factories (phytoremediation) are considered as cost-effective and environmentally-friendly bioremediation. In addition, recent advances in genetic modifications and biotechnology have been used to develop (i) more efficient transgenic microbes and plants that can (hyper)accumulate or detoxify arsenic, and (ii) novel organo-mineral materials for more efficient arsenic remediation. In this review, the most recent insights from arsenic bio-/phytoremediation are presented, and the most relevant physiological and molecular mechanisms involved in arsenic biological routes, which can be useful starting points in the creation of more arsenic-tolerant microbes and plants, as well as their symbiotic associations are discussed.
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Lee HS, Lee SY, Yoo K, Kim HW, Lee E, Im NG. Biohydrogen production and purification: Focusing on bioelectrochemical systems. BIORESOURCE TECHNOLOGY 2022; 363:127956. [PMID: 36115508 DOI: 10.1016/j.biortech.2022.127956] [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: 08/02/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Innovative technologies on green hydrogen production become significant as the hydrogen economy has grown globally. Biohydrogen is one of green hydrogen production methods, and microbial electrochemical cells (MECs) can be key to biohydrogen provision. However, MECs are immature for biohydrogen technology due to several limitations including extracellular electron transfer (EET) engineering. Fundamental understanding of EET also needs more works to accelerate MEC commercialization. Interestingly, studies on biohydrogen gas purification are limited although biohydrogen gas mixture requires complex purification for use. To facilitate an MEC-based biohydrogen technology as the green hydrogen supply this review discussed EET kinetics, engineering of EET and direct interspecies electron transfer associated with hydrogen yield and the application of advanced molecular biology for improving EET kinetics. Finally, this article reviewed biohydrogen purification technologies to better understand purification and use appropriate for biohydrogen, focusing on membrane separation.
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Affiliation(s)
- Hyung-Sool Lee
- KENTECH Institute for Environmental and Climate Technology, Korea Institute of Energy Technology (KENTECH), 200 Hyeoksin-ro, Naju-si, Jeollanam-do, South Korea.
| | - Soo Youn Lee
- Gwangju Clean Energy Research Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, South Korea
| | - Hyo Won Kim
- KENTECH Institute for Environmental and Climate Technology, Korea Institute of Energy Technology (KENTECH), 200 Hyeoksin-ro, Naju-si, Jeollanam-do, South Korea
| | - Eunseok Lee
- KENTECH Institute for Environmental and Climate Technology, Korea Institute of Energy Technology (KENTECH), 200 Hyeoksin-ro, Naju-si, Jeollanam-do, South Korea
| | - Nam Gyu Im
- KENTECH Institute for Environmental and Climate Technology, Korea Institute of Energy Technology (KENTECH), 200 Hyeoksin-ro, Naju-si, Jeollanam-do, South Korea
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Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability. ENVIRONMENTAL RESEARCH 2022; 211:113102. [PMID: 35300964 DOI: 10.1016/j.envres.2022.113102] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023]
Abstract
Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur-208001, India.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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8
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Yuan J, Li Q, Zhao Y. The research trend on arsenic pollution in freshwater: a bibliometric review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:602. [PMID: 35864315 DOI: 10.1007/s10661-022-10188-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/12/2022] [Indexed: 06/15/2023]
Abstract
We conducted a quantitative and qualitative bibliometric analysis based on 8740 research articles from the Web of Science Core Collection published in the last 20 years (2000-2020) for a better understanding of the research progress and development trend of arsenic pollution in freshwater (FAP). The results showed a significant increase in the number of publications from 2007 to 2020, especially after 2015. Four of the top 10 productive authors are from China. Two of the top three research institutions are from China, and the publications of Chinese Academy of Sciences accounted for 5.40% of the total. China is also the center of the national cooperation network, indicating a greater influence of China in this scientific research field. The top three journals included Science of the Total Environmental, Environmental Science Technology, and Journal of Hazardous Materials. Besides arsenic, the high-frequency keywords in this field included adsorption, contamination, groundwater, removal, detection, and geochemistry. The researchers mainly focused on the groundwater environment, as well as the pollution hazards of arsenic in water bodies, remediation techniques, detection, migration, and transformation. Studies should pay more attention to the application and development of phytoremediation technology in the field of FAP in the future.
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Affiliation(s)
- Jie Yuan
- Wuhan Library, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Hubei Key Laboratory of Big Data in Science and Technology, Wuhan, 430074, People's Republic of China
| | - Qianxi Li
- Hubei Provincial Academy of Eco-Environmental Sciences, Wuhan, 430074, People's Republic of China
| | - Yanqiang Zhao
- Wuhan Library, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Hubei Key Laboratory of Big Data in Science and Technology, Wuhan, 430074, People's Republic of China.
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9
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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Zounemat-Kermani M, Alizamir M, Keshtegar B, Batelaan O, Hinkelmann R. Prediction of effluent arsenic concentration of wastewater treatment plants using machine learning and kriging-based models. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:20556-20570. [PMID: 34739667 DOI: 10.1007/s11356-021-16916-6] [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: 03/23/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
This study evaluates the potential of kriging-based (kriging and kriging-logistic) and machine learning models (MARS, GBRT, and ANN) in predicting the effluent arsenic concentration of a wastewater treatment plant. Two distinct input combination scenarios were established, using seven quantitative and qualitative independent influent variables. In the first scenario, all of the seven independent variables were taken into account for constructing the data-driven models. For the second input scenario, the forward selection k-fold cross-validation method was employed to select effective explanatory influent parameters. The results obtained from both input scenarios show that the kriging-logistic and machine learning models are effective and robust. However, using the feature selection procedure in the second scenario not only made the architecture of the model simpler and more effective, but also enhanced the performance of the developed models (e.g., around 7.8% performance enhancement of the RMSE). Although the standard kriging method provided the least good predictive results (RMSE = 0.18 ug/l and NSE=0.75), it was revealed that the kriging-logistic method gave the best performance among the applied models (RMSE = 0.11 ug/l and NSE=0.90).
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Affiliation(s)
- Mohammad Zounemat-Kermani
- Department of Water Engineering, Shahid Bahonar University of Kerman, Kerman, Iran.
- Center of Excellence in Hydroinformatics, University of Tabriz, 29 Bahman Ave, Tabriz, Iran.
| | - Meysam Alizamir
- Department of Civil Engineering, Hamedan branch, Islamic Azad University, Hamedan, Iran
| | - Behrooz Keshtegar
- Department of Civil Engineering, Faculty of Engineering, University of Zabol, P.B. 9861335-856, Zabol, Iran
| | - Okke Batelaan
- National Centre for Groundwater Research and Training, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Reinhard Hinkelmann
- Chair of Water Resources Management and Modeling of Hydrosystems, Technische Universität Berlin, Berlin, Germany
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11
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
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Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis. Res Microbiol 2020; 171:37-43. [DOI: 10.1016/j.resmic.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022]
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Dunivin TK, Yeh SY, Shade A. A global survey of arsenic-related genes in soil microbiomes. BMC Biol 2019; 17:45. [PMID: 31146755 PMCID: PMC6543643 DOI: 10.1186/s12915-019-0661-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/02/2019] [Indexed: 01/21/2023] Open
Abstract
Background Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. Results We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. Conclusions Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes. Electronic supplementary material The online version of this article (10.1186/s12915-019-0661-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taylor K Dunivin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.,Environmental and Integrative Toxicological Sciences Doctoral Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Susanna Y Yeh
- Institute for Cyber-Enabled Research, Michigan State University, East Lansing, MI, 48824, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA. .,Plant Resilience Institute, Michigan State University, East Lansing, MI, 48834, USA.
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Crognale S, Casentini B, Amalfitano S, Fazi S, Petruccioli M, Rossetti S. Biological As(III) oxidation in biofilters by using native groundwater microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:93-102. [PMID: 30227294 DOI: 10.1016/j.scitotenv.2018.09.176] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L-1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.
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Affiliation(s)
- Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Barbara Casentini
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Stefano Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Stefano Fazi
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Agroforestry and Biological systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy.
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Jaiswal S, Singh DK, Shukla P. Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review. Front Microbiol 2019; 10:87. [PMID: 30853940 PMCID: PMC6396717 DOI: 10.3389/fmicb.2019.00087] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/16/2019] [Indexed: 01/15/2023] Open
Abstract
Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Dileep Kumar Singh
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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