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Ng TL, Silver PA. Sustainable B 12-Dependent Dehalogenation of Organohalides in E. coli. ACS Chem Biol 2024; 19:380-391. [PMID: 38254247 DOI: 10.1021/acschembio.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial bioremediation can provide an environmentally friendly and scalable solution to treat contaminated soil and water. However, microbes have yet to optimize pathways for degrading persistent anthropogenic pollutants, in particular organohalides. In this work, we first expand our repertoire of enzymes useful for bioremediation. By screening a panel of cobalamin (B12)-dependent reductive dehalogenases, we identified previously unreported enzymes that dechlorinate perchloroethene and regioselectively deiodinate the thyroidal disruptor 2,4,6-triiodophenol. One deiodinase, encoded by the animal-associated anaerobe Clostridioides difficile, was demonstrated to dehalogenate the naturally occurring metabolites L-halotyrosines. In cells, several combinations of ferredoxin oxidoreductase and flavodoxin extract and transfer low-potential electrons from pyruvate to drive reductive dehalogenation without artificial reductants and mediators. This work provides new insights into a relatively understudied family of B12-dependent enzymes and sets the stage for engineering synthetic pathways for degrading unnatural small molecule pollutants.
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Affiliation(s)
- Tai L Ng
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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2
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Barathi S, J G, Rathinasamy G, Sabapathi N, Aruljothi KN, Lee J, Kandasamy S. Recent trends in polycyclic aromatic hydrocarbons pollution distribution and counteracting bio-remediation strategies. CHEMOSPHERE 2023; 337:139396. [PMID: 37406936 DOI: 10.1016/j.chemosphere.2023.139396] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/21/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are distributed worldwide due to long-term anthropogenic pollution sources. PAHs are recalcitrant and highly persistent in the environment due to their inherent properties, such as heterocyclic aromatic ring structures, thermostability, and hydrophobicity. They are highly toxic, carcinogenic, immunotoxic, teratogenic, and mutagenic to various life systems. This review focuses on the unique data of PAH sources, exposure routes, detection techniques, and harmful effects on the environment and human health. This review provides a comprehensive and systematic compilation of eco-friendly biological treatment solutions for PAH remediation, such as microbial remediation approaches utilizing microbial cultures. In situ and Ex situ bioremediation of PAH methods, including composting land farming, biopiles, bioreactors bioaugmentation, and phytoremediation processes, are discussed in detail, as is a summary of the factors affecting and limiting PAH bioremediation. This review provides an overview of emerging technologies that use multi-process combinatorial treatment approaches and answers to generating value-added by-products during PAH remediation.
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Affiliation(s)
- Selvaraj Barathi
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Gitanjali J
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 63014, Tamil Nadu, India
| | - Gandhimathi Rathinasamy
- Department of Pharmaceutical Chemistry and Analysis, School of Pharmaceutical Sciences, Vels Institute of Science, Technology & Advanced Studies (VISTAS), Pallavaram, Chennai, 600117, Tamilnadu, India
| | - Nadana Sabapathi
- Centre of Translational Research, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518107, China
| | - K N Aruljothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, India
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Sabariswaran Kandasamy
- Department of Biotechnology, PSGR Krishnammal College for Women, Peelamedu, Coimbatore, 641004, India.
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3
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Huo K, Wang S, Zhao W, Guo H, Xiong W, Liu R, Yang C. Creating an efficient 1,2-dichloroethane-mineralizing bacterium by a combination of pathway engineering and promoter engineering. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163140. [PMID: 37001652 DOI: 10.1016/j.scitotenv.2023.163140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023]
Abstract
Currently, 1,2-dichloroethane (DCA) is frequently detected in groundwater and has been listed as a potential human carcinogen by the U.S. EPA. Owing to its toxicity and recalcitrant nature, inefficient DCA mineralization has become a bottleneck of DCA bioremediation. In this study, the first engineered DCA-mineralizing strain KTU-P8DCA was constructed by functional assembly of DCA degradation pathway and enhancing pathway expression with a strong promoter P8 in the biosafety strain Pseudomonas putida KT2440. Strain KTU-P8DCA can metabolize DCA to produce CO2 and utilize DCA as the sole carbon source for cell growth by quantifying 13C stable isotope ratios in collected CO2 and in lyophilized cells. Strain KTU-P8DCA exhibited superior tolerance to high concentrations of DCA. Excellent genetic stability was also observed in continuous passage culture. Therefore, strain KTU-P8DCA has enormous potential for use in bioremediation of sites heavily contaminated with DCA. In the future, our strategy for pathway construction and optimization is expected to be developed as a standard pipeline for creating a wide variety of new contaminants-mineralizing microorganisms. The present study also highlights the power of synthetic biology in creating novel degraders for environmental remediation.
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Affiliation(s)
- Kaiyue Huo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Siqi Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hongfu Guo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weini Xiong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ruihua Liu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Li B, Xu D, Zhou X, Yin Y, Feng L, Liu Y, Zhang L. Environmental behaviors of emerging contaminants in freshwater ecosystem dominated by submerged plants: A review. ENVIRONMENTAL RESEARCH 2023; 227:115709. [PMID: 36933641 DOI: 10.1016/j.envres.2023.115709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/25/2023] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
Persistent exposure of emerging contaminants (ECs) in freshwater ecosystem has initiated intense global concerns. Freshwater ecosystem dominated by submerged plants (SP-FES) has been widely constructed to control eutrophic water. However, the environmental behaviors (e.g. migration, transformation, and degradation) of ECs in SP-FES have rarely been concerned and summarized. This review briefly introduced the sources of ECs, the pathways of ECs entering into SP-FES, and the constituent elements of SP-FES. And then the environmental behaviors of dissolved ECs and refractory solid ECs in SP-FES were comprehensively summarized, and the feasibility of removing ECs from SP-FES was critically evaluated. Finally, the challenges and perspectives on the future development for ECs removal from SP-FES were prospected, giving possible research gaps and key directions. This review will provide theoretical and technical support for the effective removal of ECs in freshwater ecosystem, especially in SP-FES.
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Affiliation(s)
- Benhang Li
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China; School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Dandan Xu
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhou
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Yijun Yin
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Li Feng
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Yongze Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Liqiu Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China.
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5
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Vijayanand M, Ramakrishnan A, Subramanian R, Issac PK, Nasr M, Khoo KS, Rajagopal R, Greff B, Wan Azelee NI, Jeon BH, Chang SW, Ravindran B. Polyaromatic hydrocarbons (PAHs) in the water environment: A review on toxicity, microbial biodegradation, systematic biological advancements, and environmental fate. ENVIRONMENTAL RESEARCH 2023; 227:115716. [PMID: 36940816 DOI: 10.1016/j.envres.2023.115716] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/04/2023] [Accepted: 03/16/2023] [Indexed: 05/08/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are considered a major class of organic contaminants or pollutants, which are poisonous, mutagenic, genotoxic, and/or carcinogenic. Due to their ubiquitous occurrence and recalcitrance, PAHs-related pollution possesses significant public health and environmental concerns. Increasing the understanding of PAHs' negative impacts on ecosystems and human health has encouraged more researchers to focus on eliminating these pollutants from the environment. Nutrients available in the aqueous phase, the amount and type of microbes in the culture, and the PAHs' nature and molecular characteristics are the common factors influencing the microbial breakdown of PAHs. In recent decades, microbial community analyses, biochemical pathways, enzyme systems, gene organization, and genetic regulation related to PAH degradation have been intensively researched. Although xenobiotic-degrading microbes have a lot of potential for restoring the damaged ecosystems in a cost-effective and efficient manner, their role and strength to eliminate the refractory PAH compounds using innovative technologies are still to be explored. Recent analytical biochemistry and genetically engineered technologies have aided in improving the effectiveness of PAHs' breakdown by microorganisms, creating and developing advanced bioremediation techniques. Optimizing the key characteristics like the adsorption, bioavailability, and mass transfer of PAH boosts the microorganisms' bioremediation performance, especially in the natural aquatic water bodies. This review's primary goal is to provide an understanding of recent information about how PAHs are degraded and/or transformed in the aquatic environment by halophilic archaea, bacteria, algae, and fungi. Furthermore, the removal mechanisms of PAH in the marine/aquatic environment are discussed in terms of the recent systemic advancements in microbial degradation methodologies. The review outputs would assist in facilitating the development of new insights into PAH bioremediation.
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Affiliation(s)
- Madhumitha Vijayanand
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India
| | - Abiraami Ramakrishnan
- Department of Civil Engineering, Christian College of Engineering and Technology Oddanchatram, 624619,Dindigul District, Tamilnadu, India
| | - Ramakrishnan Subramanian
- Department of Civil Engineering, Sri Krishna College of Engineering and Technology, Kuniamuthur, Coimbatore, 641008, Tamilnadu, India
| | - Praveen Kumar Issac
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India.
| | - Mahmoud Nasr
- Environmental Engineering Department, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, 21934, Egypt; Sanitary Engineering Department, Faculty of Engineering, Alexandria University, 21544, Alexandria, Egypt
| | - Kuan Shiong Khoo
- Biorefinery and Bioprocess Engineering Laboratory, Department of Chemical Engineering and Material Science, Yuan Ze University, Taoyuan, Taiwan
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Babett Greff
- Department of Food Science, Albert Casimir Faculty at Mosonmagyaróvár, Széchenyi István University, 15-17 Lucsony Street, 9200, Mosonmagyaróvár, Hungary
| | - Nur Izyan Wan Azelee
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor Darul Takzim, Malaysia
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Soon Woong Chang
- Department of Environmental Energy & Engineering, Kyonggi University, Suwon-si, Gyeonggi-do, 16227, South Korea
| | - Balasubramani Ravindran
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India; Department of Environmental Energy & Engineering, Kyonggi University, Suwon-si, Gyeonggi-do, 16227, South Korea.
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6
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Chakravorty M, Nanda M, Bisht B, Sharma R, Kumar S, Mishra A, Vlaskin MS, Chauhan PK, Kumar V. Heavy metal tolerance in microalgae: Detoxification mechanisms and applications. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 260:106555. [PMID: 37196506 DOI: 10.1016/j.aquatox.2023.106555] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
The proficiency of microalgae to resist heavy metals has potential to be beneficial in resolving various environmental challenges. Global situations such as the need for cost-effective and ecological ways of remediation of contaminated water and for the development of bioenergy sources could employ microalgae. In a medium with the presence of heavy metals, microalgae utilize different mechanisms to uptake the metal and further detoxify it. Biosorption and the next process of bioaccumulation are two such major steps and they also include the assistance of different transporters at different stages of heavy metal tolerance. This capability has also proved to be efficient in eradicating many heavy metals like Chromium, Copper, Lead, Arsenic, Mercury, Nickel and Cadmium from the environment they are present in. This indicates the possibility of the application of microalgae as a biological way of remediating contaminated water. Heavy metal resistance quality also allows various microalgal species to contribute in the generation of biofuels like biodiesel and biohydrogen. Many research works have also explored the capacity of microalgae in nanotechnology for the formation of nanoparticles due to its relevant characteristics. Various studies have also revealed that biochar deduced from microalgae or a combination of biochar and microalgae can have wide applications specially in deprivation of heavy metals from an environment. This review focuses on the strategies adopted by microalgae, various transporters involved in the process of tolerating heavy metals and the applications where microalgae can participate owing to its ability to resist metals.
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Affiliation(s)
- Manami Chakravorty
- Department of Biotechnology, Dolphin (PG) Institute of Biomedical & Natural Sciences, Dehradun-248007, India
| | - Manisha Nanda
- Department of Biotechnology, Dolphin (PG) Institute of Biomedical & Natural Sciences, Dehradun-248007, India
| | - Bhawna Bisht
- Algal Research and Bioenergy Lab, Department of Food Science and Technology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Rohit Sharma
- School of Engineering, University of Petroleum and Energy Studies, Dehradun, India
| | - Sanjay Kumar
- Algal Research and Bioenergy Lab, Department of Food Science and Technology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Abhilasha Mishra
- Department of Chemistry, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Mikhail S Vlaskin
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 13/2 Izhorskaya St, Moscow 125412, Russian Federation
| | - P K Chauhan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, HP, India
| | - Vinod Kumar
- Algal Research and Bioenergy Lab, Department of Food Science and Technology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India; Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russian Federation.
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7
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Hassanien A, Saadaoui I, Schipper K, Al-Marri S, Dalgamouni T, Aouida M, Saeed S, Al-Jabri HM. Genetic engineering to enhance microalgal-based produced water treatment with emphasis on CRISPR/Cas9: A review. Front Bioeng Biotechnol 2023; 10:1104914. [PMID: 36714622 PMCID: PMC9881887 DOI: 10.3389/fbioe.2022.1104914] [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: 11/22/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023] Open
Abstract
In recent years, the increased demand for and regional variability of available water resources, along with sustainable water supply planning, have driven interest in the reuse of produced water. Reusing produced water can provide important economic, social, and environmental benefits, particularly in water-scarce regions. Therefore, efficient wastewater treatment is a crucial step prior to reuse to meet the requirements for use within the oil and gas industry or by external users. Bioremediation using microalgae has received increased interest as a method for produced water treatment for removing not only major contaminants such as nitrogen and phosphorus, but also heavy metals and hydrocarbons. Some research publications reported nearly 100% removal of total hydrocarbons, total nitrogen, ammonium nitrogen, and iron when using microalgae to treat produced water. Enhancing microalgal removal efficiency as well as growth rate, in the presence of such relevant contaminants is of great interest to many industries to further optimize the process. One novel approach to further enhancing algal capabilities and phytoremediation of wastewater is genetic modification. A comprehensive description of using genetically engineered microalgae for wastewater bioremediation is discussed in this review. This article also reviews random and targeted mutations as a method to alter microalgal traits to produce strains capable of tolerating various stressors related to wastewater. Other methods of genetic engineering are discussed, with sympathy for CRISPR/Cas9 technology. This is accompanied by the opportunities, as well as the challenges of using genetically engineered microalgae for this purpose.
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Affiliation(s)
- Alaa Hassanien
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar,Biological and environmental Sciences Department, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Kira Schipper
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | | | - Tasneem Dalgamouni
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, Qatar Foundation, College of Health and Life Sciences, Education City, Hamad Bin Khalifa University, Doha, Qatar
| | - Suhur Saeed
- ExxonMobil Research Qatar (EMRQ), Doha, Qatar
| | - Hareb M. Al-Jabri
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar,Biological and environmental Sciences Department, College of Arts and Sciences, Qatar University, Doha, Qatar,*Correspondence: Hareb M. Al-Jabri,
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8
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Bokade P, Gaur VK, Tripathi V, Bobate S, Manickam N, Bajaj A. Bacterial remediation of pesticide polluted soils: Exploring the feasibility of site restoration. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129906. [PMID: 36088882 DOI: 10.1016/j.jhazmat.2022.129906] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
For decades, reclamation of pesticide contaminated sites has been a challenging avenue. Due to increasing agricultural demand, the application of synthetic pesticides could not be controlled in its usage, and it has now adversely impacted the soil, water, and associated ecosystems posing adverse effects on human health. Agricultural soil and pesticide manufacturing sites, in particular, are one of the most contaminated due to direct exposure. Among various strategies for soil reclamation, ecofriendly microbial bioremediation suffers inherent challenges for large scale field application as interaction of microbes with the polluted soil varies greatly under climatic conditions. Methodically, starting from functional or genomic screening, enrichment isolation; functional pathway mapping, production of tensioactive metabolites for increasing the bioavailability and bio-accessibility, employing genetic engineering strategies for modifications in existing catabolic genes to enhance the degradation activity; each step-in degradation study has challenges and prospects which can be addressed for successful application. The present review critically examines the methodical challenges addressing the feasibility for restoring and reclaiming pesticide contaminated sites along with the ecotoxicological risk assessments. Overall, it highlights the need to fine-tune the available processes and employ interdisciplinary approaches to make microbe assisted bioremediation as the method of choice for reclamation of pesticide contaminated sites.
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Affiliation(s)
- Priyanka Bokade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; School of Energy and Chemical Engineering, UNIST, Ulsan 44919, South Korea
| | - Varsha Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Shishir Bobate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Natesan Manickam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol 2023; 11:1178680. [PMID: 37122866 PMCID: PMC10133563 DOI: 10.3389/fbioe.2023.1178680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.
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Antony S, Antony S, Rebello S, George S, Biju DT, R R, Madhavan A, Binod P, Pandey A, Sindhu R, Awasthi MK. Bioremediation of Endocrine Disrupting Chemicals- Advancements and Challenges. ENVIRONMENTAL RESEARCH 2022; 213:113509. [PMID: 35660566 DOI: 10.1016/j.envres.2022.113509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/08/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Endocrine Disrupting Chemicals (EDCs), major group of recalcitrant compounds, poses a serious threat to the health and future of millions of human beings, and other flora and fauna for years to come. A close analysis of various xenobiotics undermines the fact that EDC is structurally diverse chemical compounds generated as a part of anthropogenic advancements as well as part of their degradation. Regardless of such structural diversity, EDC is common in their ultimate drastic effect of impeding the proper functioning of the endocrinal system, basic physiologic systems, resulting in deregulated growth, malformations, and cancerous outcomes in animals as well as humans. The current review outlines an overview of various EDCs, their toxic effects on the ecosystem and its inhabitants. Conventional remediation methods such as physico-chemical methods and enzymatic approaches have been put into action as some form of mitigation measures. However, the last decade has seen the hunt for newer technologies and methodologies at an accelerated pace. Genetically engineered microbial degradation, gene editing strategies, metabolic and protein engineering, and in-silico predictive approaches - modern day's additions to our armamentarium in combating the EDCs are addressed. These additions have greater acceptance socially with lesser dissonance owing to reduced toxic by-products, lower health trepidations, better degradation, and ultimately the prevention of bioaccumulation. The positive impact of such new approaches on controlling the menace of EDCs has been outlaid. This review will shed light on sources of EDCs, their impact, significance, and the different remediation and bioremediation approaches, with a special emphasis on the recent trends and perspectives in using sustainable approaches for bioremediation of EDCs. Strict regulations to prevent the release of estrogenic chemicals to the ecosystem, adoption of combinatorial methods to remove EDC and prevalent use of bioremediation techniques should be followed in all future endeavors to combat EDC pollution. Moreover, the proper development, growth and functioning of future living forms relies on their non-exposure to EDCs, thus remediation of such chemicals present even in nano-concentrations should be addressed gravely.
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Affiliation(s)
- Sherly Antony
- Department of Microbiology, Pushpagiri Institute of Medical Sciences and Research Centre, Thiruvalla, 689 101, Kerala, India
| | - Sham Antony
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Sharrel Rebello
- School of Food Science & Technology, Mahatma Gandhi University, Kottayam, India
| | - Sandhra George
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Devika T Biju
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Reshmy R
- Department of Science and Humanities, Providence College of Engineering, Chengannur, 689 122, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum, 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, Kerala, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India; Centre for Energy and Environmental Sustainability, Lucknow, 226 029, Uttar Pradesh, India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, 691 505, Kerala, India.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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11
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Bala S, Garg D, Thirumalesh BV, Sharma M, Sridhar K, Inbaraj BS, Tripathi M. Recent Strategies for Bioremediation of Emerging Pollutants: A Review for a Green and Sustainable Environment. TOXICS 2022; 10:toxics10080484. [PMID: 36006163 PMCID: PMC9413587 DOI: 10.3390/toxics10080484] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 05/04/2023]
Abstract
Environmental pollution brought on by xenobiotics and other related recalcitrant compounds have recently been identified as a major risk to both human health and the natural environment. Due to their toxicity and non-biodegradability, a wide range of pollutants, such as heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals are present in the environment. Bioremediation is an effective cleaning technique for removing toxic waste from polluted environments that is gaining popularity. Various microorganisms, including aerobes and anaerobes, are used in bioremediation to treat contaminated sites. Microorganisms play a major role in bioremediation, given that it is a process in which hazardous wastes and pollutants are eliminated, degraded, detoxified, and immobilized. Pollutants are degraded and converted to less toxic forms, which is a primary goal of bioremediation. Ex situ or in situ bioremediation can be used, depending on a variety of factors, such as cost, pollutant types, and concentration. As a result, a suitable bioremediation method has been chosen. This review focuses on the most recent developments in bioremediation techniques, how microorganisms break down different pollutants, and what the future holds for bioremediation in order to reduce the amount of pollution in the world.
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Affiliation(s)
- Saroj Bala
- Department of Microbiology, Punjab Agriculture University, Ludhiana 141001, India
| | - Diksha Garg
- Department of Microbiology, Punjab Agriculture University, Ludhiana 141001, India
| | - Banjagere Veerabhadrappa Thirumalesh
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Minaxi Sharma
- Laboratoire de Chimie Verte et Produits Biobasés, Département Agro Bioscience et Chimie, Haute Ecole Provinciale de Hainaut-Condorcet, 11 Rue de la Sucrerie, 7800 Ath, Belgium
| | - Kandi Sridhar
- UMR1253, Science et Technologie du Lait et de l’œuf, INRAE, L’Institut Agro Rennes-Angers, 65 Rue de Saint Brieuc, F-35042 Rennes, France
| | - Baskaran Stephen Inbaraj
- Department of Food Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
- Correspondence: (B.S.I.); (M.T.)
| | - Manikant Tripathi
- Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya 224001, India
- Correspondence: (B.S.I.); (M.T.)
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12
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Muneeswari R, Iyappan S, Swathi KV, Vinu R, Ramani K, Sekaran G. Biocatalytic lipoprotein bioamphiphile induced treatment of recalcitrant hydrocarbons in petroleum refinery oil sludge through transposon technology. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128520. [PMID: 35228072 DOI: 10.1016/j.jhazmat.2022.128520] [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: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The present investigation employed transposon technology to enhance the degradation of recalcitrant petroleum hydrocarbons present in petroleum oil sludge by using biosurfactant hyper-producing strain Enterobacter xiangfangensis STP-3. Out of 2500 transposon induced mutants, mutants M257E.xiangfangensis and M916E.xiangfangensis hyper-produce biocatalytic lipoprotein biosurfactant by1.98 and 2.34 fold higher than wild-type strain. Transposon induced mutation also modified the amino acid composition which improved the hydrophobicity and thermal stability of the biosurfactants produced by mutants, compared to the wild-type biosurfactant. GC-MS and LC-MS-MS revealed that biosurfactants have pentameric lipid moiety and esterase as protein moiety. Increased biosurfactant hydrophobicity and yield by the mutants resulted in the enhanced bioavailability of petroleum hydrocarbons, thereby mutants M257E.xiangfangensis and M916E.xiangfangensis demonstrated better petroleum oil sludge degradation by 82% and 88% respectively, than wild-type (72%). Disrupted genes vgr G and pgm M in M257E.xiangfangensis and M916E.xiangfangensis respectively hyper-produce biosurfactant by competitive pathway inhibition and increased precursor availability mechanism. Hyper-production of biosurfactant was also validated by comparing the expression of biosynthetic genes ent E, ent F and est using qPCR. This is the first report on the application of transposon technology to hyper-produce biosurfactant for the effective bioremediation of hydrocarbon contaminated environments.
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Affiliation(s)
- R Muneeswari
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - S Iyappan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - K V Swathi
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - R Vinu
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Ramani
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India.
| | - G Sekaran
- SRM Institute of Science and Technology, Ramapuram 600089, Tamil Nadu, India
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13
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Martínez BCS, Benavides LM, Santoyo G, Sánchez-Yáñez JM. Biorecovery of Agricultural Soil Impacted by Waste Motor Oil with Phaseolus vulgaris and Xanthobacter autotrophicus. PLANTS (BASEL, SWITZERLAND) 2022; 11:1419. [PMID: 35684191 PMCID: PMC9182674 DOI: 10.3390/plants11111419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Agricultural soil contamination by waste motor oil (WMO) is a worldwide environmental problem. The phytotoxicity of WMO hydrocarbons limits agricultural production; therefore, Mexican standard NOM-138-SEMARNAT/SSA1-2012 (NOM-138) establishes a maximum permissible limit of 4400 ppm for hydrocarbons in soil. The objectives of this study are to (a) biostimulate, (b) bioaugment, and (c) phytoremediate soil impacted by 60,000 ppm of WMO, to decrease it to a concentration lower than the maximum allowed by NOM-138. Soil contaminated with WMO was biostimulated, bioaugmented, and phytoremediated, and the response variables were WMO concentration, germination, phenology, and biomass of Phaseolus vulgaris. The experimental data were validated by Tukey HSD ANOVA. The maximum decrease in WMO was recorded in the soil biostimulated, bioaugmented, and phytoremediated by P. vulgaris from 60,000 ppm to 190 ppm, which was considerably lower than the maximum allowable limit of 4400 ppm of NOM-138 after five months. Biostimulation of WMO-impacted soil by detergent, mineral solution and bioaugmentation with Xanthobacter autotrophicus accelerated the reduction in WMO concentration, which allowed phytoremediation with P. vulgaris to oxidize aromatic hydrocarbons and recover WMO-impacted agricultural soil faster than other bioremediation strategies.
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Adeola AO, Ore OT, Fapohunda O, Adewole AH, Akerele DD, Akingboye AS, Oloye FF. Psychotropic Drugs of Emerging Concerns in Aquatic Systems: Ecotoxicology and Remediation Approaches. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00334-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Ahmad HA, Ahmad S, Cui Q, Wang Z, Wei H, Chen X, Ni SQ, Ismail S, Awad HM, Tawfik A. The environmental distribution and removal of emerging pollutants, highlighting the importance of using microbes as a potential degrader: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151926. [PMID: 34838908 DOI: 10.1016/j.scitotenv.2021.151926] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Emerging pollutants (EPs) create a worldwide concern owing to their low concentration and severe toxicity to the receptors. The prominent emerging pollutants categories as pharmaceutical and personal care product, plasticizer, surfactants, and persistent organic pollutants. Typically, EPs are widely disseminated in the aquatic ecosystem and capable of perturbing the physiology of water bodies as well as humans. The primary sources of EPs in the environment include anthropogenic release, atmospheric deposition, untreated or substandard treated wastewater, and extreme weather events. Intensive research has been done covering the environmental distribution, ecological disturbance, fate, and removal of EPs in the past decades. However, a systematic review on the distribution of EPs in the engineered and natural aquatic environment and the degradation of different EPs by using anaerobic sludge, aerobic bacteria, and isolated strains are limited. This review article aims to highlight the importance, application, and future perceptions of using different microbes to degrade EPs. Overall, this review article illustrates the superiority of using non-cultivable and cultivable microbes to degrade the EPs as an eco-friendly approach. Practically, the outcomes of this review paper will build up the knowledge base solutions to remove EPs from the wastewater.
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Affiliation(s)
- Hafiz Adeel Ahmad
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China; Suzhou Research Institute, Shandong University, Suzhou, Jiangsu 215123, China; Shenzhen Research Institute, Shandong University, Shenzhen, Guangdong 518052, China
| | - Shakeel Ahmad
- Department of Soil and Environmental Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Qingjie Cui
- Department of Mechanical and Environmental Protection, Shandong Electric Power Engineering Consulting Institute Ltd. (SDEPCI), Jinan, Shandong 250013, China
| | - Zhibin Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Haiwei Wei
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Xue Chen
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Shou-Qing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China; Suzhou Research Institute, Shandong University, Suzhou, Jiangsu 215123, China; Shenzhen Research Institute, Shandong University, Shenzhen, Guangdong 518052, China.
| | - Sherif Ismail
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China; Environmental Engineering Department, Zagazig University, Zagazig 44519, Egypt
| | - Hanem M Awad
- National Research Centre, Tanning Materials & Proteins Department, Dokki, Giza 12622, Egypt
| | - Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, Dokki, Giza 12622, Egypt
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16
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Tang Q, Aslan-Üzel AS, Schuiten ED, Badenhorst CPS, Pavlidis IV, Bornscheuer UT. Enzymatic Photometric Assays for the Selective Detection of Halides. Methods Mol Biol 2022; 2487:361-375. [PMID: 35687247 DOI: 10.1007/978-1-0716-2269-8_22] [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] [Indexed: 06/15/2023]
Abstract
Halides are substrates and products of a number of biotechnologically important enzymes like dehalogenases, halide methyltransferases, and halogenases. Therefore, the determination of halide concentrations in samples is important. The classical methods based on mercuric thiocyanate are very dangerous, produce hazardous waste, and do not discriminate between chloride, bromide, and iodide. In this chapter, we describe a detailed protocol for the determination of halide concentrations based on the haloperoxidase-catalyzed oxidation of halides. The resulting hypohalous acids are detected using commercially available colorimetric or fluorimetric probes. The biocatalytic nature of the assays allows them to be implemented in one-pot cascade reactions with halide-generating enzymes. Since chloride is ubiquitous in biological systems, we also describe convenient photometric assays for the selective detection of bromide and iodide in the presence of chloride, obviating the need for laborious dialyses to obtain halide-free enzymes and reagents.
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Affiliation(s)
- Qingyun Tang
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Askin S Aslan-Üzel
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Eva D Schuiten
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | | | | | - Uwe T Bornscheuer
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
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17
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Yeung CS, Tse HY, Lau CY, Guan J, Huang J, Phillips DL, Leu SY. Insights into unexpected photoisomerization from photooxidation of tribromoacetic acid in aqueous environment using ultrafast spectroscopy. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126214. [PMID: 34102359 DOI: 10.1016/j.jhazmat.2021.126214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Haloacetic acids are carcinogenic disinfection by-products (DPBs) and their photo-decomposition pathways, especially for those containing bromine and iodine, are not fully understood. In this study, femtosecond transient absorption (fs-TA) spectroscopy experiments were introduced for the first time to investigate the photochemistry of tribromoacetic acid. The fs-TA experiments showed that a photoisomerization intermediate species HOOCCBr2-Br (iso-TBAA) was formed within several picoseconds after the excitation of TBAA. The absorption wavelength of the iso-TBAA was supported by time-dependent density calculations. With the Second-order Møller-Plesset perturbation theory, the structures and thermodynamics of the OH-insertion reactions of iso-TBAA were elucidated when water molecules were involved in the reaction complex. The calculations also revealed that the isomer species were able to react with water with its reaction dynamics dramatically catalyzed by the hydrogen bonding network. The proposed water catalyzed OH-insertion/HBr elimination mechanism predicted three major photoproducts, namely, HBr, CO and CO2, which was consistent with the photolysis experiments with firstly reported CO formation rate and mass conversion yield as 0.096 min-1 and 0.75 ± 0.1 respectively. The spectroscopic technique, numerical tool and disclosed mechanisms provided insights on photodecomposition and subsequent reactions of polyhalo-DPBs contain heavy atom(s) (e.g., Br, I) with water, aliphatic alcohols or other nucleophiles.
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Affiliation(s)
- Chi Shun Yeung
- Department of Civil & Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Ho-Yin Tse
- Department of Civil & Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Chun Yin Lau
- Department of Civil & Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Jianyu Guan
- Department of Civil & Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong.
| | - Shao-Yuan Leu
- Department of Civil & Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong.
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18
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Sharma P, Sirohi R, Tong YW, Kim SH, Pandey A. Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125855. [PMID: 34492804 DOI: 10.1016/j.jhazmat.2021.125855] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.
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Affiliation(s)
- Pooja Sharma
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Sang Hyoun Kim
- Department of Chemical and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India.
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19
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Singh AK, Bilal M, Iqbal HMN, Meyer AS, Raj A. Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145988. [PMID: 33684751 DOI: 10.1016/j.scitotenv.2021.145988] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Anne S Meyer
- Department for Biotechnology and Biomedicine, Technical University of Denmark, Building 221, DK-2800 Lyngby, Denmark.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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20
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Singh AK, Bilal M, Iqbal HMN, Raj A. Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144561. [PMID: 33736422 DOI: 10.1016/j.scitotenv.2020.144561] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 02/05/2023]
Abstract
The feasibility of in-silico techniques, together with the computational framework, has been applied to predictive bioremediation aiming to clean-up contaminants, toxicity evaluation, and possibilities for the degradation of complex recalcitrant compounds. Emerging contaminants from different industries have posed a significant hazard to the environment and public health. Given current bioremediation strategies, it is often a failure or inadequate for sustainable mitigation of hazardous pollutants. However, clear-cut vital information about biodegradation is quite incomplete from a conventional remediation techniques perspective. Lacking complete information on bio-transformed compounds leads to seeking alternative methods. Only scarce information about the transformed products and toxicity profile is available in the published literature. To fulfill this literature gap, various computational or in-silico technologies have emerged as alternating techniques, which are being recognized as in-silico approaches for bioremediation. Molecular docking, molecular dynamics simulation, and biodegradation pathways predictions are the vital part of predictive biodegradation, including the Quantitative Structure-Activity Relationship (QSAR), Quantitative structure-biodegradation relationship (QSBR) model system. Furthermore, machine learning (ML), artificial neural network (ANN), genetic algorithm (GA) based programs offer simultaneous biodegradation prediction along with toxicity and environmental fate prediction. Herein, we spotlight the feasibility of in-silico remediation approaches for various persistent, recalcitrant contaminants while traditional bioremediation fails to mitigate such pollutants. Such could be addressed by exploiting described model systems and algorithm-based programs. Furthermore, recent advances in QSAR modeling, algorithm, and dedicated biodegradation prediction system have been summarized with unique attributes.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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21
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Behrendorff JBYH. Reductive Cytochrome P450 Reactions and Their Potential Role in Bioremediation. Front Microbiol 2021; 12:649273. [PMID: 33936006 PMCID: PMC8081977 DOI: 10.3389/fmicb.2021.649273] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 enzymes, or P450s, are haem monooxygenases renowned for their ability to insert one atom from molecular oxygen into an exceptionally broad range of substrates while reducing the other atom to water. However, some substrates including many organohalide and nitro compounds present little or no opportunity for oxidation. Under hypoxic conditions P450s can perform reductive reactions, contributing electrons to drive reductive elimination reactions. P450s can catalyse dehalogenation and denitration of a range of environmentally persistent pollutants including halogenated hydrocarbons and nitroamine explosives. P450-mediated reductive dehalogenations were first discovered in the context of human pharmacology but have since been observed in a variety of organisms. Additionally, P450-mediated reductive denitration of synthetic explosives has been discovered in bacteria that inhabit contaminated soils. This review will examine the distribution of P450-mediated reductive dehalogenations and denitrations in nature and discuss synthetic biology approaches to developing P450-based reagents for bioremediation.
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Affiliation(s)
- James B. Y. H. Behrendorff
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, Canberra, ACT, Australia
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22
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Haskett TL, Tkacz A, Poole PS. Engineering rhizobacteria for sustainable agriculture. THE ISME JOURNAL 2021; 15:949-964. [PMID: 33230265 PMCID: PMC8114929 DOI: 10.1038/s41396-020-00835-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.
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Affiliation(s)
- Timothy L. Haskett
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Andrzej Tkacz
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Philip S. Poole
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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Mishra S, Lin Z, Pang S, Zhang W, Bhatt P, Chen S. Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities. Front Bioeng Biotechnol 2021; 9:632059. [PMID: 33644024 PMCID: PMC7902726 DOI: 10.3389/fbioe.2021.632059] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.
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Affiliation(s)
- 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziqiu Lin
- 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shimei Pang
- 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wenping Zhang
- 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Gul I, Le W, Jie Z, Ruiqin F, Bilal M, Tang L. Recent advances on engineered enzyme-conjugated biosensing modalities and devices for halogenated compounds. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Lamraoui I, Eltoukhy A, Wang J, Lamraoui M, Ahmed A, Jia Y, Lu T, Yan Y. Biodegradation of Di (2-Ethylhexyl) Phthalate by a novel Enterobacter spp. Strain YC-IL1 Isolated from Polluted Soil, Mila, Algeria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17207501. [PMID: 33076331 PMCID: PMC7602616 DOI: 10.3390/ijerph17207501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/09/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is one of the phthalic acid ester representatives and is mainly used as a plasticizer to endow polyvinyl chloride plastics with desirable physical properties. It is synthesized in massive amounts worldwide. Many studies have proved the adverse effects of DEHP on human health and wildlife. DEHP is labeled as an endocrine disruptor which causes human reproductive problems. Enterobacter spp. YC-IL1, a novel isolated strain from contaminated soil, was identified by 16S rRNA gene analysis and electronic microscope. It is capable of efficiently degrading DEHP (100%) and a wide range of phthalic acid ester PAEs, particularly those containing side chains with branches, or ring structures such as dutylbenzyl phthalate and dicyclohexyl phthalate, which are hard to degrade, with, respectively, 81.15% and 50.69% degradation after 7 days incubation. YC-IL1 is an acido-tolerant strain which remained in pH values lower than pH 5.0 with the optimum pH 7.0 and temperature 30 °C. The DEHP metabolites were detected using HPLC-QQQ and then the degradation pathway was tentatively proposed. Strain YC-IL1 showed high DEHP degradation rate in artificially contaminated soil with 86% removed in 6 days. These results indicate the application potential of YC-IL1 in bioremediation of PAE-polluted sites, even the acidic ones.
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Affiliation(s)
- Imane Lamraoui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (I.L.); (T.L.)
| | - Adel Eltoukhy
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt;
| | - Junhuan Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (Y.J.)
| | - Messaouda Lamraoui
- Department of Microbiology, Faculty of Nature Science and Life, University of Bejaia, Bejaia 0600, Algeria;
| | - Amer Ahmed
- Department of Life Sciences, University of Siena, 53100 Siena, Italy;
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (Y.J.)
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (I.L.); (T.L.)
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (Y.J.)
- Correspondence: ; Tel.: +86-10-8210-9685
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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: 57] [Impact Index Per Article: 14.3] [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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